#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	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_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	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_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	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_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	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
MIOS	54468	hgsc.bcm.edu	37	7	7622772	7622772	+	Missense_Mutation	SNP	A	A	C			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											105.0	106.0	105.0					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	
THSD7A	221981	hgsc.bcm.edu	37	7	11676072	11676072	+	Missense_Mutation	SNP	G	G	A			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											32.0	32.0	32.0					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	
GLI3	2737	hgsc.bcm.edu	37	7	42004065	42004065	+	Missense_Mutation	SNP	A	A	G	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											101.0	97.0	98.0					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	
PKD1L1	168507	hgsc.bcm.edu	37	7	47937659	47937659	+	Missense_Mutation	SNP	C	C	T	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	99.0	87.0	91.0		2197	-1.8	0.0	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	
POM121L12	285877	hgsc.bcm.edu	37	7	53103958	53103958	+	Silent	SNP	C	C	T			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											49.0	58.0	55.0					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	
FZD9	8326	hgsc.bcm.edu	37	7	72848698	72848698	+	Missense_Mutation	SNP	C	C	T			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											7.0	7.0	7.0					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		
AKAP9	10142	hgsc.bcm.edu	37	7	91726163	91726163	+	Missense_Mutation	SNP	A	A	G			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											107.0	104.0	105.0					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	
TRRAP	8295	hgsc.bcm.edu	37	7	98592257	98592257	+	Silent	SNP	G	G	A			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											181.0	174.0	176.0					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	
COG5	10466	hgsc.bcm.edu	37	7	106964917	106964917	+	Missense_Mutation	SNP	G	G	A			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											49.0	58.0	55.0					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		
MET	4233	hgsc.bcm.edu	37	7	116423415	116423415	+	Silent	SNP	T	T	C			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											105.0	98.0	100.0					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		
CLEC2L	154790	hgsc.bcm.edu	37	7	139225207	139225207	+	Missense_Mutation	SNP	G	G	C			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											13.0	17.0	15.0					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	
BRAF	673	hgsc.bcm.edu	37	7	140453105	140453105	+	Silent	SNP	A	A	G			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											101.0	93.0	95.0					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	
EPHB6	2051	hgsc.bcm.edu	37	7	142566734	142566734	+	Missense_Mutation	SNP	A	A	G			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											35.0	32.0	33.0					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		
SSPO	23145	hgsc.bcm.edu	37	7	149482248	149482248	+	RNA	SNP	T	T	C			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											99.0	106.0	103.0					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			
LRRC61	65999	hgsc.bcm.edu	37	7	150034184	150034184	+	Silent	SNP	T	T	C	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	49.0	46.0	47.0		234,234	-7.1	0.0	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	
ABCF2	10061	hgsc.bcm.edu	37	7	150921028	150921028	+	Silent	SNP	A	A	G			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											77.0	71.0	73.0					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	
KIAA1755	85449	hgsc.bcm.edu	37	20	36845803	36845803	+	Missense_Mutation	SNP	T	T	C			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											35.0	30.0	32.0					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	
TP53TG5	27296	hgsc.bcm.edu	37	20	44004158	44004158	+	Missense_Mutation	SNP	T	T	C	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											65.0	37.0	46.0					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	
NPEPL1	79716	hgsc.bcm.edu	37	20	57289017	57289017	+	Silent	SNP	C	C	T	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	13.0	20.0	18.0		1086,1026,1170	-2.9	1.0	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	
SS18L1	26039	hgsc.bcm.edu	37	20	60738562	60738562	+	Missense_Mutation	SNP	A	A	G			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											31.0	34.0	33.0					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		
LAMA5	3911	hgsc.bcm.edu	37	20	60898720	60898720	+	Silent	SNP	C	C	T	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	0.0115	5008	,	,		14154	0.0		0.0288	False		,,,				2504	0.002																0			20						C		31,4353		0,31,2161	18.0	25.0	22.0		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	
LAMA5	3911	hgsc.bcm.edu	37	20	60909381	60909381	+	Missense_Mutation	SNP	T	T	A			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											26.0	27.0	26.0					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	
DIDO1	11083	hgsc.bcm.edu	37	20	61513408	61513408	+	Silent	SNP	A	A	G			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											70.0	77.0	74.0					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	
COL20A1	57642	hgsc.bcm.edu	37	20	61957486	61957486	+	Silent	SNP	A	A	C	rs67798234|rs142285603|rs397706060		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.chr20:61957486A>C	ENST00000358894.6	+	30	3541	c.3441A>C	c.(3439-3441)ggA>ggC	p.G1147G	COL20A1_ENST00000326996.6_Silent_p.G1179G|COL20A1_ENST00000435874.1_Silent_p.G1154G|COL20A1_ENST00000422202.1_Silent_p.G1154G	NM_020882.2	NP_065933.2	Q9P218	COKA1_HUMAN	collagen, type XX, alpha 1	1147	Collagen-like 2.				extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)				NS(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(21)|ovary(1)|prostate(3)|urinary_tract(2)	36	all_cancers(38;1.39e-10)					GCCTGCCTGGACCCCCTGGCC	0.652																																																	0			20											51.0	60.0	57.0					20																	61957486		1930	4125	6055	61427931	SO:0001819	synonymous_variant	57642			BC043183	CCDS46628.1	20q13.33	2014-02-12			ENSG00000101203	ENSG00000101203		"""Collagens"", ""Fibronectin type III domain containing"""	14670	protein-coding gene	gene with protein product						10819331	Standard	NM_020882		Approved	KIAA1510	uc011aau.2	Q9P218	OTTHUMG00000032964	ENST00000358894.6:c.3441A>C	20.37:g.61957486A>C			61427931	Q4VXQ4|Q6PI59|Q8WUT2|Q96CY9|Q9BQU6|Q9BQU7	Silent	SNP	ENST00000358894.6	37	CCDS46628.1																																																																																				0.652	COL20A1-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000144595.2	NM_020882	
ZDHHC8	29801	hgsc.bcm.edu	37	22	20134739	20134739	+	3'UTR	SNP	C	C	T	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	
YDJC	150223	hgsc.bcm.edu	37	22	21984205	21984205	+	Silent	SNP	A	A	G	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	18.0	17.0	17.0		99	-8.9	0.0	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		
YPEL1	29799	hgsc.bcm.edu	37	22	22064927	22064927	+	Missense_Mutation	SNP	A	A	T			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											312.0	265.0	281.0					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	
ADRBK2	157	hgsc.bcm.edu	37	22	26091119	26091119	+	Silent	SNP	G	G	A			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											181.0	158.0	166.0					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	
BPIFC	254240	hgsc.bcm.edu	37	22	32853314	32853314	+	Silent	SNP	G	G	A			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											130.0	120.0	123.0					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	
MIA2	117153	hgsc.bcm.edu	37	14	39717088	39717088	+	Missense_Mutation	SNP	A	A	G			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											58.0	65.0	62.0					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	
HEATR4	399671	hgsc.bcm.edu	37	14	73959403	73959403	+	Intron	SNP	A	A	G			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											55.0	61.0	59.0					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	
TSHR	7253	hgsc.bcm.edu	37	14	81610293	81610293	+	Missense_Mutation	SNP	T	T	C	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						214.0	189.0	197.0					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	
PRIMA1	145270	hgsc.bcm.edu	37	14	94245652	94245652	+	Silent	SNP	C	C	T	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	40.0	34.0	36.0		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	
POLRMT	5442	hgsc.bcm.edu	37	19	622336	622336	+	Missense_Mutation	SNP	T	T	G	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	3.0	4.0	4.0		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	
SPPL2B	56928	hgsc.bcm.edu	37	19	2344022	2344022	+	RNA	SNP	G	G	A	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	33.0	36.0	35.0		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	
CDKN2D	1032	hgsc.bcm.edu	37	19	10676423	10676423	+	IGR	SNP	G	G	A	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	17.0	18.0	18.0		156	2.1	1.0	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	
DNM2	1785	hgsc.bcm.edu	37	19	10906754	10906754	+	Missense_Mutation	SNP	C	C	T			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											118.0	118.0	118.0					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	
RGL3	57139	hgsc.bcm.edu	37	19	11527625	11527625	+	Missense_Mutation	SNP	G	G	A	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	72.0	69.0	70.0		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	
BEST2	54831	hgsc.bcm.edu	37	19	12866196	12866196	+	Missense_Mutation	SNP	C	C	A			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											114.0	113.0	114.0					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	
CYP4F12	66002	hgsc.bcm.edu	37	19	15807034	15807034	+	Splice_Site	SNP	A	A	G			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											101.0	104.0	103.0					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
KIAA1683	80726	hgsc.bcm.edu	37	19	18377048	18377048	+	Silent	SNP	C	C	G			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											86.0	80.0	82.0					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		
ZNF676	163223	hgsc.bcm.edu	37	19	22363649	22363649	+	Silent	SNP	G	G	T			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											98.0	103.0	102.0					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	
CYP2A7	1549	hgsc.bcm.edu	37	19	41386527	41386527	+	Missense_Mutation	SNP	G	G	A	rs58798281	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.chr19:41386527G>A	ENST00000301146.4	-	3	891	c.350C>T	c.(349-351)gCg>gTg	p.A117V	CTC-490E21.12_ENST00000601627.1_Intron|CYP2A7_ENST00000291764.3_Missense_Mutation_p.A66V	NM_000764.2	NP_000755.2	P20853	CP2A7_HUMAN	cytochrome P450, family 2, subfamily A, polypeptide 7	117						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)			GTTGCTGAACGCCACGCCTGG	0.697													.|||	2594	0.517971	0.4244	0.6729	5008	,	,		9286	0.4405		0.5169	False		,,,				2504	0.6155																0			19											14.0	14.0	14.0					19																	41386527		2154	4177	6331	46078367	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.350C>T	19.37:g.41386527G>A	ENSP00000301146:p.Ala117Val		46078367	Q13121	Missense_Mutation	SNP	ENST00000301146.4	37	CCDS12569.1	919	0.4207875457875458	156	0.3170731707317073	218	0.6022099447513812	234	0.4090909090909091	311	0.4102902374670185	N	0.051	-1.248973	0.01469	.	.	ENSG00000198077	ENST00000301146;ENST00000291764	T;T	0.67865	-0.29;-0.29	2.16	1.06	0.20224	.	0.670270	0.14526	N	0.314179	T	0.00012	0.0000	N	0.04387	-0.21	0.80722	P	0.0	B;B;B	0.15473	0.013;0.011;0.001	B;B;B	0.17979	0.02;0.016;0.013	T	0.45279	-0.9272	9	0.08599	T	0.76	.	8.261	0.31786	0.2665:0.0:0.7335:0.0	rs58798281	117;66;117	B7ZKR0;F8W816;P20853	.;.;CP2A7_HUMAN	V	117;66	ENSP00000301146:A117V;ENSP00000291764:A66V	ENSP00000291764:A66V	A	-	2	0	CYP2A7	46078367	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-0.684000	0.05173	-0.117000	0.11872	-1.514000	0.00941	GCG		0.697	CYP2A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463269.2	NM_030589	
ZNF574	64763	hgsc.bcm.edu	37	19	42583249	42583249	+	Missense_Mutation	SNP	C	C	T			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											52.0	61.0	58.0					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	
ZNF574	64763	hgsc.bcm.edu	37	19	42584961	42584961	+	Missense_Mutation	SNP	C	C	T			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											71.0	81.0	78.0					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	
ZNF234	10780	hgsc.bcm.edu	37	19	44652970	44652970	+	Missense_Mutation	SNP	A	A	G			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											199.0	198.0	198.0					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		
LILRA2	11027	hgsc.bcm.edu	37	19	55098716	55098716	+	Missense_Mutation	SNP	G	G	A	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	0.0	5008	,	,		20282	0.0		0.001	False		,,,				2504	0.0																0			19											122.0	106.0	111.0					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		
CCDC106	29903	hgsc.bcm.edu	37	19	56162681	56162681	+	Missense_Mutation	SNP	C	C	T	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	28.0	32.0	30.0		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	
ZNF471	57573	hgsc.bcm.edu	37	19	57036518	57036518	+	Missense_Mutation	SNP	T	T	C			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											73.0	78.0	76.0					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	
ZNF154	7710	hgsc.bcm.edu	37	19	58216252	58216252	+	Missense_Mutation	SNP	C	C	T			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											174.0	166.0	168.0					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		
SLC27A5	10998	hgsc.bcm.edu	37	19	59011992	59011992	+	Missense_Mutation	SNP	G	G	A			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											97.0	91.0	93.0					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	
CSMD1	64478	hgsc.bcm.edu	37	8	2807758	2807758	+	Missense_Mutation	SNP	C	C	T			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											156.0	158.0	157.0					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	
NEIL2	252969	hgsc.bcm.edu	37	8	11637447	11637447	+	Missense_Mutation	SNP	A	A	G			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											55.0	58.0	57.0					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	
FGF17	8822	hgsc.bcm.edu	37	8	21903639	21903639	+	Silent	SNP	G	G	A	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											60.0	64.0	63.0					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	
ESCO2	157570	hgsc.bcm.edu	37	8	27650248	27650248	+	Missense_Mutation	SNP	C	C	T			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											56.0	56.0	56.0					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	
PRKDC	5591	hgsc.bcm.edu	37	8	48805818	48805818	+	Splice_Site	SNP	T	T	G			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											27.0	28.0	28.0					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
XKR4	114786	hgsc.bcm.edu	37	8	56435861	56435861	+	Missense_Mutation	SNP	T	T	C			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											50.0	48.0	49.0					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	
CA3	761	hgsc.bcm.edu	37	8	86358404	86358404	+	Missense_Mutation	SNP	T	T	C			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											42.0	35.0	37.0					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	
RUNX1T1	862	hgsc.bcm.edu	37	8	93004062	93004062	+	Nonsense_Mutation	SNP	G	G	A	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											168.0	140.0	150.0					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	
LAPTM4B	55353	hgsc.bcm.edu	37	8	98788261	98788261	+	Silent	SNP	G	G	T	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		0.1471	False		,,,				2504	0.1319																0			8						G		258,4118		11,236,1941	18.0	20.0	19.0		297	0.8	1.0	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		
TNFRSF11B	4982	hgsc.bcm.edu	37	8	119964052	119964052	+	Missense_Mutation	SNP	G	G	C	rs2073618	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.chr8:119964052G>C	ENST00000297350.4	-	1	387	c.9C>G	c.(7-9)aaC>aaG	p.N3K		NM_002546.3	NP_002537.3	O00300	TR11B_HUMAN	tumor necrosis factor receptor superfamily, member 11b	3			N -> K (in dbSNP:rs2073618). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:9108485, ECO:0000269|PubMed:9492069, ECO:0000269|PubMed:9688283, ECO:0000269|Ref.6}.		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)			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)			AGCACAGCAAGTTGTTCATTG	0.682													C|||	3339	0.666733	0.9236	0.4654	5008	,	,		12595	0.7609		0.4672	False		,,,				2504	0.5706																0			8	GRCh37	CM045665	TNFRSF11B	M	rs2073618	C	LYS/ASN	3767,613		1621,525,44	17.0	18.0	18.0		9	5.3	0.8	8	dbSNP_96	18	3863,4713		867,2129,1292	yes	missense	TNFRSF11B	NM_002546.3	94	2488,2654,1336	CC,CG,GG		45.0443,13.9954,41.1084	benign	3/402	119964052	7630,5326	2190	4288	6478	120033233	SO:0001583	missense	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.9C>G	8.37:g.119964052G>C	ENSP00000297350:p.Asn3Lys		120033233	B2R9A8|O60236|Q53FX6|Q9UHP4	Missense_Mutation	SNP	ENST00000297350.4	37	CCDS6326.1	1406	0.6437728937728938	436	0.8861788617886179	183	0.505524861878453	425	0.743006993006993	362	0.47757255936675463	C	7.688	0.690394	0.15039	0.860046	0.450443	ENSG00000164761	ENST00000297350	T	0.71579	-0.58	5.26	5.26	0.73747	.	0.637813	0.16792	N	0.199355	T	0.00012	0.0000	N	0.00347	-1.61	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.36138	-0.9760	8	.	.	.	-1.0265	11.9629	0.53019	0.0:0.826:0.174:0.0	rs2073618;rs17751701;rs60810341;rs2073618	3	O00300	TR11B_HUMAN	K	3	ENSP00000297350:N3K	.	N	-	3	2	TNFRSF11B	120033233	0.032000	0.19561	0.781000	0.31783	0.965000	0.64279	0.645000	0.24782	1.474000	0.48178	-0.335000	0.08231	AAC		0.682	TNFRSF11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381220.1		
COL14A1	7373	hgsc.bcm.edu	37	8	121322277	121322277	+	Silent	SNP	C	C	A			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											154.0	137.0	143.0					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	
GRINA	2907	hgsc.bcm.edu	37	8	145065646	145065646	+	Silent	SNP	A	A	C			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											3.0	4.0	4.0					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	
MMP23B	8510	hgsc.bcm.edu	37	1	1571841	1571841	+	IGR	SNP	A	A	C	rs150949339	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.chr1:1571841A>C	ENST00000356026.5	+	0	1326				CDK11B_ENST00000317673.7_Missense_Mutation_p.D641E|CDK11B_ENST00000340677.5_Missense_Mutation_p.D630E|CDK11B_ENST00000341832.6_Missense_Mutation_p.D596E|CDK11B_ENST00000407249.3_Missense_Mutation_p.D643E			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.D643E(3)		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)	GGGTCCCCAGATCCTGAAAGA	0.577																																																	3	Substitution - Missense(3)	haematopoietic_and_lymphoid_tissue(1)|lung(1)|central_nervous_system(1)	1						A	GLU/ASP,GLU/ASP,GLU/ASP,GLU/ASP,GLU/ASP,GLU/ASP	663,3183		0,663,1260	41.0	40.0	40.0		1665,1152,1554,1563,1683,1656	2.6	1.0	1	dbSNP_134	40	156,8096		0,156,3970	no	missense,missense,missense,missense,missense,missense	CDK11B	NM_033486.1,NM_033487.1,NM_033488.1,NM_033489.1,NM_033492.1,NM_033493.1	45,45,45,45,45,45	0,819,5230	CC,CA,AA		1.8905,17.2387,6.7697	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	555/698,384/527,518/661,521/664,561/704,552/695	1571841	819,11279	1923	4126	6049	1561704	SO:0001628	intergenic_variant	0				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.1571841A>C			1561704	A2AGN0|A2AGN1|O75894|O75895|Q5QPQ8|Q76P96|Q7LDM6|Q7LDM7|Q9UBR9|Q9UJK8	Missense_Mutation	SNP	ENST00000356026.5	37	CCDS30559.1																																																																																				0.577	MMP23B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158492.2	NM_006983	
RUNX3	864	hgsc.bcm.edu	37	1	25245749	25245749	+	Missense_Mutation	SNP	C	C	T			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											72.0	64.0	67.0					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	
SDC3	9672	hgsc.bcm.edu	37	1	31346158	31346158	+	Missense_Mutation	SNP	C	C	T			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											123.0	104.0	111.0					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	
CSMD2	114784	hgsc.bcm.edu	37	1	34204921	34204921	+	Missense_Mutation	SNP	C	C	T			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											79.0	82.0	81.0					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	
KDM4A	9682	hgsc.bcm.edu	37	1	44121267	44121267	+	Silent	SNP	T	T	C			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											109.0	103.0	105.0					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	
DPH2	1802	hgsc.bcm.edu	37	1	44435855	44435855	+	Missense_Mutation	SNP	C	C	T			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											45.0	45.0	45.0					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	
CYP4X1	260293	hgsc.bcm.edu	37	1	47512207	47512207	+	Missense_Mutation	SNP	T	T	C			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											182.0	154.0	164.0					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	
ZCCHC11	23318	hgsc.bcm.edu	37	1	52991354	52991354	+	Missense_Mutation	SNP	C	C	T			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											189.0	193.0	192.0					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	
SLC44A3	126969	hgsc.bcm.edu	37	1	95310926	95310926	+	Silent	SNP	T	T	C			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											116.0	121.0	119.0					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	
AGL	178	hgsc.bcm.edu	37	1	100343240	100343240	+	Silent	SNP	C	C	T			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											103.0	100.0	101.0					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	
GPR61	83873	hgsc.bcm.edu	37	1	110086198	110086198	+	Missense_Mutation	SNP	A	A	G			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											160.0	143.0	149.0					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		
KCNC4	3749	hgsc.bcm.edu	37	1	110754500	110754500	+	Missense_Mutation	SNP	G	G	A			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											45.0	51.0	49.0					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	
CTTNBP2NL	55917	hgsc.bcm.edu	37	1	112999695	112999695	+	Silent	SNP	T	T	C			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											133.0	120.0	125.0					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	
RSBN1	54665	hgsc.bcm.edu	37	1	114354942	114354942	+	Silent	SNP	T	T	G	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	21.0	29.0	27.0	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	
IGSF3	3321	hgsc.bcm.edu	37	1	117142868	117142868	+	Nonsense_Mutation	SNP	C	C	T	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											34.0	39.0	37.0					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	
FLG	2312	hgsc.bcm.edu	37	1	152280433	152280433	+	Missense_Mutation	SNP	G	G	C			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											236.0	271.0	259.0					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	
FLG2	388698	hgsc.bcm.edu	37	1	152327667	152327667	+	Silent	SNP	C	C	T	rs12738471	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.chr1:152327667C>T	ENST00000388718.5	-	3	2667	c.2595G>A	c.(2593-2595)tcG>tcA	p.S865S	FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000445097.1_RNA	NM_001014342.2	NP_001014364.1	Q5D862	FILA2_HUMAN	filaggrin family member 2	865	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)			ATGTCTGTCCCGAACTTGACC	0.502													c|||	787	0.157149	0.0091	0.2565	5008	,	,		24019	0.3373		0.0696	False		,,,				2504	0.1912																0			1											377.0	328.0	344.0					1																	152327667		2203	4294	6497	150594291	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.2595G>A	1.37:g.152327667C>T			150594291	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	
DENND4B	9909	hgsc.bcm.edu	37	1	153907297	153907297	+	Silent	SNP	C	C	T	rs557071025|rs544489048	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.chr1:153907297C>T	ENST00000361217.4	-	18	3130	c.2712G>A	c.(2710-2712)caG>caA	p.Q904Q	DENND4B_ENST00000474386.1_5'Flank	NM_014856.2	NP_055671.2	O75064	DEN4B_HUMAN	DENN/MADD domain containing 4B	904	Gln-rich.				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)			gctgctgctgctgctgctgtt	0.632													c|||	1	0.000199681	0.0	0.0	5008	,	,		16455	0.0		0.0	False		,,,				2504	0.001																0			1											28.0	36.0	33.0					1																	153907297		2179	4277	6456	152173921	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.2712G>A	1.37:g.153907297C>T			152173921	Q5T4K0	Silent	SNP	ENST00000361217.4	37	CCDS44228.1																																																																																				0.632	DENND4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090278.2	XM_375806	
PVRL4	81607	hgsc.bcm.edu	37	1	161044047	161044047	+	Nonsense_Mutation	SNP	G	G	A			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											184.0	164.0	171.0					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	
LHX4	89884	hgsc.bcm.edu	37	1	180241067	180241067	+	Missense_Mutation	SNP	G	G	A			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											70.0	80.0	77.0					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	
CHIT1	1118	hgsc.bcm.edu	37	1	203192643	203192643	+	Missense_Mutation	SNP	G	G	A	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	78.0	79.0	79.0		460	2.9	0.0	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	
PLXNA2	5362	hgsc.bcm.edu	37	1	208211813	208211813	+	Missense_Mutation	SNP	C	C	T	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	82.0	71.0	75.0		4667	4.8	1.0	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	
TMEM206	55248	hgsc.bcm.edu	37	1	212538603	212538603	+	Missense_Mutation	SNP	T	T	C			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											222.0	213.0	216.0					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	
PSEN2	5664	hgsc.bcm.edu	37	1	227073296	227073296	+	Silent	SNP	C	C	T			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											200.0	133.0	156.0					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	
RYR2	6262	hgsc.bcm.edu	37	1	237993876	237993876	+	Missense_Mutation	SNP	T	T	G			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											217.0	204.0	208.0					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	
FMN2	56776	hgsc.bcm.edu	37	1	240370998	240370998	+	Silent	SNP	A	A	G	rs199866405	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.chr1:240370998A>G	ENST00000319653.9	+	5	3116	c.2886A>G	c.(2884-2886)gcA>gcG	p.A962A		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	962	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)			TTCCCGGGGCAGGCATACCCC	0.697																																																	0			1											21.0	23.0	23.0					1																	240370998		2200	4297	6497	238437621	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.2886A>G	1.37:g.240370998A>G			238437621	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Silent	SNP	ENST00000319653.9	37	CCDS31069.2																																																																																				0.697	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352	
FMN2	56776	hgsc.bcm.edu	37	1	240371484	240371484	+	Silent	SNP	A	A	T	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											8.0	10.0	9.0					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	
NLRP6	171389	hgsc.bcm.edu	37	11	280790	280790	+	Missense_Mutation	SNP	G	G	T			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											48.0	51.0	50.0					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	
PHRF1	57661	hgsc.bcm.edu	37	11	609068	609068	+	Silent	SNP	G	G	A	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	9.0	11.0	10.0		3609	-9.3	0.0	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	
CRACR2B	283229	hgsc.bcm.edu	37	11	830670	830670	+	Missense_Mutation	SNP	G	G	T	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	3.0	5.0	5.0		743	1.0	1.0	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		
KRTAP5-5	439915	hgsc.bcm.edu	37	11	1651119	1651119	+	Missense_Mutation	SNP	C	C	T			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.chr11:1651119C>T	ENST00000399676.2	+	1	87	c.49C>T	c.(49-51)Cgt>Tgt	p.R17C		NM_001001480.2	NP_001001480.2	Q701N2	KRA55_HUMAN	keratin associated protein 5-5	17				R -> L (in Ref. 1; BAD20201 and 2; CAF31639). {ECO:0000305}.		keratin filament (GO:0045095)		p.R17C(2)		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)		ctgtggaggccgtggctccgg	0.692																																																	2	Substitution - Missense(2)	lung(1)|endometrium(1)	11											50.0	63.0	58.0					11																	1651119		2186	4288	6474	1607695	SO:0001583	missense	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.49C>T	11.37:g.1651119C>T	ENSP00000382584:p.Arg17Cys		1607695	A8MWN2	Missense_Mutation	SNP	ENST00000399676.2	37	CCDS41592.1	.	.	.	.	.	.	.	.	.	.	c	4.536	0.099454	0.08681	.	.	ENSG00000185940	ENST00000399676;ENST00000422553	T	0.00840	5.63	2.63	-0.0442	0.13856	.	.	.	.	.	T	0.00271	0.0008	N	0.00017	-2.845	0.25377	N	0.988648	B	0.09022	0.002	B	0.01281	0.0	T	0.49380	-0.8946	9	0.62326	D	0.03	.	6.5864	0.22622	0.0:0.289:0.0:0.711	.	17	Q701N2	KRA55_HUMAN	C	17;15	ENSP00000382584:R17C	ENSP00000382584:R17C	R	+	1	0	KRTAP5-5	1607695	1.000000	0.71417	0.793000	0.32043	0.002000	0.02628	0.772000	0.26647	-0.552000	0.06167	-1.850000	0.00570	CGT		0.692	KRTAP5-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127919.1		
RRP8	23378	hgsc.bcm.edu	37	11	6621754	6621754	+	Missense_Mutation	SNP	G	G	A			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											43.0	44.0	44.0					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	
MICAL2	9645	hgsc.bcm.edu	37	11	12281386	12281386	+	Silent	SNP	T	T	C			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											54.0	54.0	54.0					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	
RRAS2	22800	hgsc.bcm.edu	37	11	14303176	14303176	+	Missense_Mutation	SNP	C	C	T			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											258.0	215.0	230.0					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	
LDHA	3939	hgsc.bcm.edu	37	11	18425274	18425274	+	Missense_Mutation	SNP	T	T	C			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											158.0	151.0	153.0					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	
PTPN5	84867	hgsc.bcm.edu	37	11	18764922	18764922	+	Missense_Mutation	SNP	C	C	T			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											137.0	130.0	132.0					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	
BDNF	627	hgsc.bcm.edu	37	11	27695763	27695763	+	5'UTR	SNP	C	C	A			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											83.0	77.0	79.0					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	
SLC39A13	91252	hgsc.bcm.edu	37	11	47435016	47435016	+	Silent	SNP	G	G	A	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	26.0	30.0	29.0		603,603	0.0	1.0	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	
CD6	923	hgsc.bcm.edu	37	11	60777073	60777073	+	Missense_Mutation	SNP	G	G	A	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	40.0	38.0	38.0		811	-9.8	0.0	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	
INCENP	3619	hgsc.bcm.edu	37	11	61897359	61897359	+	Silent	SNP	C	C	T	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	49.0	51.0	50.0		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	
C11orf95	65998	hgsc.bcm.edu	37	11	63533522	63533522	+	lincRNA	SNP	A	A	G			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.chr11:63533522A>G	ENST00000546282.2	-	0	738				C11orf95_ENST00000433688.1_lincRNA																							GTGGCCAGGGAGCTGCCGCAC	0.622																																																	0			11											110.0	102.0	104.0					11																	63533522		692	1591	2283	63290098			0																															11.37:g.63533522A>G			63290098		Missense_Mutation	SNP	ENST00000546282.2	37																																																																																					0.622	RP11-466C23.4-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000396567.2		
UNC93B1	81622	hgsc.bcm.edu	37	11	67765163	67765163	+	Splice_Site	SNP	A	A	G	rs5792426|rs112921257		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.chr11:67765163A>G	ENST00000227471.2	-	8	965	c.886T>C	c.(886-888)Ttc>Ctc	p.F296L	UNC93B1_ENST00000530331.1_5'UTR	NM_030930.2	NP_112192.2	Q9H1C4	UN93B_HUMAN	unc-93 homolog B1 (C. elegans)	297					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|intracellular protein transport (GO:0006886)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 7 signaling pathway (GO:0034154)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	early phagosome (GO:0032009)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)											ATGGCCAGGAAGCCACTGCCA	0.632																																																	0			11											34.0	44.0	41.0					11																	67765163		2133	4216	6349	67521739	SO:0001630	splice_region_variant	81622			AJ271326	CCDS73334.1	11q13.2	2014-09-17	2001-11-28		ENSG00000110057	ENSG00000110057			13481	protein-coding gene	gene with protein product		608204	"""unc93 (C. elegans) homolog B1"""			11867227	Standard	NM_030930		Approved	UNC93	uc001omw.1	Q9H1C4	OTTHUMG00000167472	ENST00000227471.2:c.886-1T>C	11.37:g.67765163A>G			67521739	O95764|Q569H6|Q710D4	Silent	SNP	ENST00000227471.2	37		.	.	.	.	.	.	.	.	.	.	.	16.46	3.130813	0.56828	.	.	ENSG00000110057	ENST00000227471	T	0.06142	3.34	4.71	4.71	0.59529	.	0.328795	0.36665	N	0.002470	T	0.04137	0.0115	N	0.14661	0.345	0.44042	D	0.99677	B	0.06786	0.001	B	0.06405	0.002	T	0.44952	-0.9294	10	0.15066	T	0.55	-41.1027	12.1477	0.54031	1.0:0.0:0.0:0.0	.	297	Q9H1C4	UN93B_HUMAN	L	296	ENSP00000227471:F296L	ENSP00000227471:F296L	F	-	1	0	UNC93B1	67521739	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.182000	0.77689	1.756000	0.51951	0.459000	0.35465	TTC		0.632	UNC93B1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_030930	Missense_Mutation
ALDH3B1	221	hgsc.bcm.edu	37	11	67789295	67789295	+	Splice_Site	SNP	G	G	C			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											34.0	40.0	38.0					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
MAML2	84441	hgsc.bcm.edu	37	11	95825407	95825407	+	Silent	SNP	C	C	T	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											28.0	35.0	33.0					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		
HTR3B	9177	hgsc.bcm.edu	37	11	113815341	113815341	+	Silent	SNP	T	T	G			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											225.0	177.0	193.0					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	
MPZL3	196264	hgsc.bcm.edu	37	11	118107936	118107936	+	Missense_Mutation	SNP	C	C	T			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											142.0	138.0	140.0					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	
ROBO4	54538	hgsc.bcm.edu	37	11	124766530	124766530	+	Missense_Mutation	SNP	A	A	G			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											34.0	38.0	37.0					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	
CHEK1	1111	hgsc.bcm.edu	37	11	125503113	125503113	+	Silent	SNP	T	T	C			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											109.0	109.0	109.0					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	
IGSF9B	22997	hgsc.bcm.edu	37	11	133806008	133806008	+	Missense_Mutation	SNP	G	G	A			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											58.0	67.0	64.0					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	
ACOT13	55856	hgsc.bcm.edu	37	6	24698112	24698112	+	Splice_Site	SNP	T	T	A			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											62.0	63.0	63.0					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
OR2B3	442184	hgsc.bcm.edu	37	6	29054978	29054978	+	Silent	SNP	G	G	T			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											77.0	75.0	76.0					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		
MUC21	394263	hgsc.bcm.edu	37	6	30954870	30954870	+	Silent	SNP	T	T	C	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											171.0	164.0	167.0					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	
DAXX	1616	hgsc.bcm.edu	37	6	33287445	33287445	+	Missense_Mutation	SNP	T	T	C			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											102.0	96.0	98.0					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		
TULP1	7287	hgsc.bcm.edu	37	6	35480009	35480009	+	Silent	SNP	C	C	T			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											4.0	5.0	5.0					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		
C6orf222	389384	hgsc.bcm.edu	37	6	36298051	36298051	+	Silent	SNP	T	T	C			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											76.0	66.0	69.0					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	
TFEB	7942	hgsc.bcm.edu	37	6	41658889	41658889	+	Silent	SNP	C	C	T	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	16.0	14.0	15.0		63,63	5.1	1.0	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		
MYO6	4646	hgsc.bcm.edu	37	6	76527363	76527363	+	Silent	SNP	C	C	G			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											74.0	72.0	72.0					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	
MRAP2	112609	hgsc.bcm.edu	37	6	84799159	84799159	+	Missense_Mutation	SNP	A	A	G			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											106.0	112.0	110.0					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	
LATS1	9113	hgsc.bcm.edu	37	6	149983274	149983274	+	Missense_Mutation	SNP	C	C	T			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											117.0	121.0	120.0					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	
AKAP12	9590	hgsc.bcm.edu	37	6	151672224	151672224	+	Missense_Mutation	SNP	A	A	G			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											58.0	65.0	63.0					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		
TCP1	6950	hgsc.bcm.edu	37	6	160209100	160209100	+	Missense_Mutation	SNP	T	T	C			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											93.0	91.0	92.0					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	
RP3-470B24.5	0	hgsc.bcm.edu	37	6	168377103	168377103	+	lincRNA	SNP	A	A	G	rs61746337		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.chr6:168377103A>G	ENST00000538528.1	-	0	516																											GGGGGAGGAGAAGACAGTGGG	0.622																																																	0			6											3.0	5.0	5.0					6																	168377103		605	1456	2061	168119952			100128124																															6.37:g.168377103A>G			168119952		Missense_Mutation	SNP	ENST00000538528.1	37																																																																																					0.622	RP3-470B24.5-201	KNOWN	basic	lincRNA	lincRNA			
RP3-470B24.5	0	hgsc.bcm.edu	37	6	168377232	168377232	+	lincRNA	SNP	A	A	G	rs202004345		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.chr6:168377232A>G	ENST00000538528.1	-	0	387																											GGAGGAGAAGACAGTGGGGGT	0.617																																																	0			6											4.0	6.0	5.0					6																	168377232		641	1510	2151	168120081			100128124																															6.37:g.168377232A>G			168120081		Missense_Mutation	SNP	ENST00000538528.1	37																																																																																					0.617	RP3-470B24.5-201	KNOWN	basic	lincRNA	lincRNA			
RP3-470B24.5	0	hgsc.bcm.edu	37	6	168377262	168377262	+	lincRNA	SNP	T	T	G	rs200098500		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.chr6:168377262T>G	ENST00000538528.1	-	0	357																											TGCAGTGTGTTGGGAGGAGGA	0.632																																																	0			6											9.0	11.0	10.0					6																	168377262		686	1579	2265	168120111			100128124																															6.37:g.168377262T>G			168120111		Missense_Mutation	SNP	ENST00000538528.1	37																																																																																					0.632	RP3-470B24.5-201	KNOWN	basic	lincRNA	lincRNA			
FRMD1	79981	hgsc.bcm.edu	37	6	168459845	168459845	+	Missense_Mutation	SNP	G	G	C	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	35.0	36.0	36.0		1162,1366	0.2	0.0	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	
YWHAE	7531	hgsc.bcm.edu	37	17	1264493	1264493	+	Silent	SNP	A	A	G			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											134.0	127.0	129.0					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	
TP53	7157	hgsc.bcm.edu	37	17	7577094	7577094	+	Missense_Mutation	SNP	G	G	A	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	83.0	71.0	75.0	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	
NF1	4763	hgsc.bcm.edu	37	17	29562747	29562747	+	Missense_Mutation	SNP	G	G	T	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						165.0	161.0	163.0					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	
KRTAP4-8	728224	hgsc.bcm.edu	37	17	39254142	39254142	+	Silent	SNP	A	A	G	rs375280428	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.chr17:39254142A>G	ENST00000333822.4	-	1	251	c.195T>C	c.(193-195)tgT>tgC	p.C65C		NM_031960.2	NP_114166.1	Q9BYQ9	KRA48_HUMAN	keratin associated protein 4-8	65	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						AGCTGGGGCGACAGCAGGTGG	0.657													G|||	2063	0.411941	0.469	0.4352	5008	,	,		13020	0.3234		0.4453	False		,,,				2504	0.3753																0			17											6.0	9.0	8.0					17																	39254142		633	1475	2108	36507668	SO:0001819	synonymous_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.195T>C	17.37:g.39254142A>G			36507668	A8MSH3	Silent	SNP	ENST00000333822.4	37	CCDS45674.1																																																																																				0.657	KRTAP4-8-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257684.1	NM_031960	
XYLT2	64132	hgsc.bcm.edu	37	17	48437547	48437547	+	Silent	SNP	T	T	C			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											41.0	38.0	39.0					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	
CACNA1G	8913	hgsc.bcm.edu	37	17	48678509	48678509	+	Missense_Mutation	SNP	C	C	T	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	79.0	78.0	79.0		3889,3820,3820,3889,3820,3889,3820,3820,3889,3889,3889,3820,3820,3820,3889	4.8	1.0	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	
ABCA8	10351	hgsc.bcm.edu	37	17	66871863	66871863	+	Missense_Mutation	SNP	C	C	T	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	0.0008	0.0	5008	,	,		19623	0.0		0.0	False		,,,				2504	0.0																0			17						C	GLN/ARG	5,4401	8.1+/-20.4	0,5,2198	64.0	52.0	56.0		4262	2.4	1.0	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	
LLGL2	3993	hgsc.bcm.edu	37	17	73567846	73567846	+	Missense_Mutation	SNP	C	C	T	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	29.0	31.0	30.0		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	
TBCD	6904	hgsc.bcm.edu	37	17	80710099	80710099	+	Silent	SNP	C	C	T	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	3.0	4.0	4.0		30	1.4	0.0	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	
SAMSN1	64092	hgsc.bcm.edu	37	21	15889299	15889299	+	Missense_Mutation	SNP	C	C	T	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	131.0	113.0	119.0		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		
TSPEAR	54084	hgsc.bcm.edu	37	21	45924706	45924706	+	Missense_Mutation	SNP	A	A	G			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											89.0	84.0	86.0					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	
KRTAP10-11	386678	hgsc.bcm.edu	37	21	46066922	46066922	+	Missense_Mutation	SNP	T	T	C	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	0.0	5008	,	,		24573	0.001		0.0	False		,,,				2504	0.0041																0			21											169.0	173.0	172.0					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	
CHTF18	63922	hgsc.bcm.edu	37	16	847845	847845	+	Missense_Mutation	SNP	C	C	T	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	0.0008	0.0	5008	,	,		7547	0.001		0.0	False		,,,				2504	0.0																0			16											14.0	19.0	17.0					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	
TBL3	10607	hgsc.bcm.edu	37	16	2025189	2025189	+	Splice_Site	SNP	T	T	C			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											86.0	91.0	89.0					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
ZNF500	26048	hgsc.bcm.edu	37	16	4802838	4802838	+	Missense_Mutation	SNP	G	G	C			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											94.0	81.0	85.0					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	
RABEP2	79874	hgsc.bcm.edu	37	16	28926022	28926022	+	Missense_Mutation	SNP	T	T	C			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											105.0	116.0	112.0					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	
SRCAP	10847	hgsc.bcm.edu	37	16	30735131	30735131	+	Silent	SNP	C	C	T			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											218.0	184.0	195.0					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	
CALB2	794	hgsc.bcm.edu	37	16	71411591	71411591	+	Missense_Mutation	SNP	G	G	A			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											109.0	98.0	101.0					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	
DHX38	9785	hgsc.bcm.edu	37	16	72135085	72135085	+	Missense_Mutation	SNP	G	G	A			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											117.0	125.0	122.0					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	
ZFHX3	463	hgsc.bcm.edu	37	16	72993831	72993831	+	Missense_Mutation	SNP	A	A	C	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	12.0	16.0	15.0		,214	5.1	1.0	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	
MPHOSPH6	10200	hgsc.bcm.edu	37	16	82203742	82203742	+	Silent	SNP	T	T	C	rs1134847	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.chr16:82203742T>C	ENST00000258169.4	-	1	89	c.39A>G	c.(37-39)ctA>ctG	p.L13L	CTD-2588J6.2_ENST00000563841.1_lincRNA|MPHOSPH6_ENST00000567729.1_5'UTR|MPHOSPH6_ENST00000563504.1_5'UTR|MPHOSPH6_ENST00000569021.1_Silent_p.L13L	NM_005792.2	NP_005783.2	Q99547	MPH6_HUMAN	M-phase phosphoprotein 6	13					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						TCATGCGCAGTAGATTCTTGG	0.711													C|||	3218	0.642572	0.4054	0.8127	5008	,	,		13310	0.7649		0.7465	False		,,,				2504	0.6094																0			16						C		2116,2282		524,1068,607	32.0	24.0	27.0		39	2.6	1.0	16	dbSNP_86	27	6335,2261		2348,1639,311	no	coding-synonymous	MPHOSPH6	NM_005792.2		2872,2707,918	CC,CT,TT		26.3029,48.1128,34.9623		13/161	82203742	8451,4543	2199	4298	6497	80761243	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.39A>G	16.37:g.82203742T>C			80761243	B2RAF0	Silent	SNP	ENST00000258169.4	37	CCDS10937.1																																																																																				0.711	MPHOSPH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269058.1	NM_005792	
MPHOSPH6	10200	hgsc.bcm.edu	37	16	82203768	82203768	+	Silent	SNP	G	G	T	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	27.0	19.0	22.0		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	
VHL	7428	hgsc.bcm.edu	37	3	10188274	10188274	+	Silent	SNP	T	T	C			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											218.0	202.0	207.0					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	
OXSM	54995	hgsc.bcm.edu	37	3	25832827	25832827	+	Missense_Mutation	SNP	T	T	C			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											170.0	144.0	153.0					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	
TGFBR2	7048	hgsc.bcm.edu	37	3	30729948	30729948	+	Missense_Mutation	SNP	A	A	G			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											126.0	117.0	120.0					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		
LRRFIP2	9209	hgsc.bcm.edu	37	3	37151154	37151154	+	Missense_Mutation	SNP	T	T	A			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											115.0	118.0	117.0					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	
ITGA9	3680	hgsc.bcm.edu	37	3	37783309	37783309	+	Splice_Site	SNP	G	G	A	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	74.0	57.0	63.0		2323	5.6	1.0	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
ACVR2B	93	hgsc.bcm.edu	37	3	38523730	38523730	+	Silent	SNP	A	A	G			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											117.0	88.0	98.0					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	
CCR1	1230	hgsc.bcm.edu	37	3	46244753	46244753	+	Missense_Mutation	SNP	A	A	G			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											50.0	48.0	48.0					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	
COL7A1	1294	hgsc.bcm.edu	37	3	48613082	48613082	+	Missense_Mutation	SNP	C	C	T	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	0.0	5008	,	,		15468	0.0		0.0	False		,,,				2504	0.0																0			3						C	LYS/GLU	4,4402	8.1+/-20.4	0,4,2199	55.0	57.0	56.0		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	
RHOA	387	hgsc.bcm.edu	37	3	49395482	49395482	+	IGR	SNP	G	G	C	rs201944086	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.chr3:49395482G>C	ENST00000418115.1	-	0	2031				GPX1_ENST00000419783.1_Missense_Mutation_p.P77R|GPX1_ENST00000419349.1_Missense_Mutation_p.P77R|GPX1_ENST00000496791.1_5'UTR	NM_001664.2	NP_001655.1	P61586	RHOA_HUMAN	ras homolog family member A						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)			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)		CTGGTTGCACGGGAAGCCGAG	0.726																																																	0			3											11.0	14.0	13.0					3																	49395482		1848	4061	5909	49370486	SO:0001628	intergenic_variant	2876			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		3.37:g.49395482G>C			49370486	P06749|Q53HM4|Q5U024|Q9UDJ0|Q9UEJ4	Missense_Mutation	SNP	ENST00000418115.1	37	CCDS2795.1	.	.	.	.	.	.	.	.	.	.	G	36	5.745728	0.96882	.	.	ENSG00000233276	ENST00000419783;ENST00000419349	T;T	0.25085	1.82;1.82	5.88	5.88	0.94601	Thioredoxin-like fold (2);	0.000000	0.85682	D	0.000000	T	0.63070	0.2480	M	0.93150	3.385	0.80722	D	1	D;D	0.71674	0.998;0.988	D;P	0.68483	0.958;0.891	T	0.72279	-0.4340	10	0.87932	D	0	.	18.8152	0.92075	0.0:0.0:1.0:0.0	.	77;77	E9PAS1;P07203	.;GPX1_HUMAN	R	77	ENSP00000407375:P77R;ENSP00000391316:P77R	ENSP00000391316:P77R	P	-	2	0	GPX1	49370486	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.875000	0.87205	2.788000	0.95919	0.555000	0.69702	CCG		0.726	RHOA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346157.3	NM_001664	
APEH	327	hgsc.bcm.edu	37	3	49723379	49723379	+	IGR	SNP	T	T	C	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											14.0	16.0	15.0					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		
ZNF717	100131827	hgsc.bcm.edu	37	3	75787280	75787280	+	Silent	SNP	T	T	C			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.chr3:75787280T>C	ENST00000478296.1	-	4	1620	c.1344A>G	c.(1342-1344)caA>caG	p.Q448Q	ZNF717_ENST00000491507.1_Intron|ZNF717_ENST00000422325.1_Silent_p.Q498Q|ZNF717_ENST00000400845.3_Silent_p.Q491Q|MIR4273_ENST00000582824.1_RNA|ZNF717_ENST00000477374.1_Intron			Q9BY31	ZN717_HUMAN	zinc finger protein 717	491					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-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(6)|endometrium(3)|lung(2)|ovary(1)|stomach(7)	19						TGTGAGTCCATTGATGGATAG	0.453																																																	0			3											1.0	1.0	1.0					3																	75787280		75	166	241	75869970	SO:0001819	synonymous_variant	100131827			AF226994		3p12.3	2013-01-08			ENSG00000227124	ENSG00000227124		"""Zinc fingers, C2H2-type"", ""-"""	29448	protein-coding gene	gene with protein product			"""zinc finger protein 838"""	ZNF838			Standard	NM_001128223		Approved	X17	uc011bgi.2	Q9BY31	OTTHUMG00000158965	ENST00000478296.1:c.1344A>G	3.37:g.75787280T>C			75869970		Silent	SNP	ENST00000478296.1	37																																																																																					0.453	ZNF717-002	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000352764.2	NM_001128223	
KIAA2018	205717	hgsc.bcm.edu	37	3	113376119	113376119	+	Silent	SNP	C	C	T	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											58.0	65.0	63.0					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	
C3orf30	152405	hgsc.bcm.edu	37	3	118865609	118865609	+	Silent	SNP	C	C	T	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	91.0	94.0	93.0		573	-8.2	0.0	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	
PTPLB	201562	hgsc.bcm.edu	37	3	123303821	123303821	+	Silent	SNP	G	G	C	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	3.0	4.0	4.0		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	
PTPLB	201562	hgsc.bcm.edu	37	3	123303824	123303824	+	Silent	SNP	A	A	G	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	2.0	4.0	4.0		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	
IFT122	55764	hgsc.bcm.edu	37	3	129214369	129214369	+	Silent	SNP	C	C	T	rs73204231		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.chr3:129214369C>T	ENST00000348417.2	+	18	2204	c.2127C>T	c.(2125-2127)gcC>gcT	p.A709A	IFT122_ENST00000507564.1_Silent_p.A701A|IFT122_ENST00000440957.2_Silent_p.A500A|IFT122_ENST00000347300.2_Silent_p.A650A|IFT122_ENST00000513932.1_3'UTR|IFT122_ENST00000296266.3_Silent_p.A760A|IFT122_ENST00000431818.2_Silent_p.A559A|IFT122_ENST00000349441.2_Silent_p.A598A|IFT122_ENST00000504021.1_Silent_p.A585A	NM_052989.1	NP_443715.1	Q9HBG6	IF122_HUMAN	intraflagellar transport 122	709					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						TCCATGAGGCCGCCAAACTGT	0.507																																																	0			3											109.0	94.0	99.0					3																	129214369		2203	4300	6503	130697059	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.2127C>T	3.37:g.129214369C>T			130697059	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	
BCHE	590	hgsc.bcm.edu	37	3	165548173	165548173	+	Missense_Mutation	SNP	G	G	T			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											80.0	85.0	84.0					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		
PIK3CA	5290	hgsc.bcm.edu	37	3	178952055	178952055	+	Missense_Mutation	SNP	A	A	G			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											96.0	85.0	88.0					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		
HTR3E	285242	hgsc.bcm.edu	37	3	183824299	183824299	+	Missense_Mutation	SNP	G	G	A			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											55.0	54.0	54.0					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	
KNG1	3827	hgsc.bcm.edu	37	3	186445055	186445055	+	Silent	SNP	C	C	T	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											104.0	107.0	106.0					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	
ITGA7	3679	hgsc.bcm.edu	37	12	56092682	56092682	+	Silent	SNP	C	C	T	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		0.0994	False		,,,				2504	0.0276																0			12						C	,,	63,4343		0,63,2140	19.0	20.0	20.0		822,531,810	4.5	1.0	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	
RBMS2	5939	hgsc.bcm.edu	37	12	56975619	56975619	+	Silent	SNP	C	C	T	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	0.0	5008	,	,		21428	0.0		0.0	False		,,,				2504	0.001																0			12						C		1,4405	2.1+/-5.4	0,1,2202	146.0	138.0	141.0		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	
MDM2	4193	hgsc.bcm.edu	37	12	69230472	69230472	+	Silent	SNP	T	T	C			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											174.0	167.0	169.0					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	
NAV3	89795	hgsc.bcm.edu	37	12	78388626	78388626	+	Missense_Mutation	SNP	G	G	A			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											136.0	128.0	131.0					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	
VSIG10	54621	hgsc.bcm.edu	37	12	118520062	118520062	+	Silent	SNP	G	G	C			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											124.0	126.0	125.0					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	
MKRN3	7681	hgsc.bcm.edu	37	15	23811330	23811330	+	Missense_Mutation	SNP	C	C	T			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											41.0	44.0	43.0					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	
RFX7	64864	hgsc.bcm.edu	37	15	56385633	56385633	+	Silent	SNP	T	T	C			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											111.0	101.0	104.0					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	
ANXA2	302	hgsc.bcm.edu	37	15	60690089	60690089	+	Intron	SNP	A	A	G	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	5.0	7.0	6.0		,24,,	-5.9	0.0	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	
CSPG4	1464	hgsc.bcm.edu	37	15	75982275	75982275	+	Silent	SNP	T	T	C	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											10.0	12.0	12.0					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	
CSPG4	1464	hgsc.bcm.edu	37	15	75982565	75982565	+	Missense_Mutation	SNP	C	C	T	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	0.0014	5008	,	,		20761	0.0		0.0	False		,,,				2504	0.0																0			15						C	ASN/ASP	1,4393		0,1,2196	51.0	45.0	47.0		841	5.0	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	
VCX2	51480	hgsc.bcm.edu	37	X	8138182	8138182	+	Missense_Mutation	SNP	A	A	G	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											27.0	34.0	32.0					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	
MAGEB4	4115	hgsc.bcm.edu	37	X	30260498	30260498	+	Silent	SNP	A	A	G			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											58.0	46.0	50.0					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	
FAM47A	158724	hgsc.bcm.edu	37	X	34148877	34148877	+	Missense_Mutation	SNP	C	C	G	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											29.0	29.0	29.0					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	
FAM47B	170062	hgsc.bcm.edu	37	X	34961532	34961532	+	Missense_Mutation	SNP	C	C	T			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											27.0	31.0	30.0					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	
FAM47C	442444	hgsc.bcm.edu	37	X	37027472	37027472	+	Missense_Mutation	SNP	T	T	C			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											84.0	77.0	80.0					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	
LANCL3	347404	hgsc.bcm.edu	37	X	37431229	37431229	+	Missense_Mutation	SNP	G	G	C	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											7.0	7.0	7.0					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	
SHROOM4	57477	hgsc.bcm.edu	37	X	50350752	50350752	+	Silent	SNP	T	T	C	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											15.0	15.0	15.0					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	
SHROOM4	57477	hgsc.bcm.edu	37	X	50350757	50350758	+	Missense_Mutation	DNP	TC	TC	GT	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	
SHROOM4	57477	hgsc.bcm.edu	37	X	50350778	50350778	+	Missense_Mutation	SNP	T	T	G	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											22.0	20.0	21.0					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	
ARHGEF9	23229	hgsc.bcm.edu	37	X	62885786	62885786	+	Missense_Mutation	SNP	G	G	T			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											102.0	80.0	88.0					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		
TEX11	56159	hgsc.bcm.edu	37	X	69825277	69825277	+	Missense_Mutation	SNP	T	T	C			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											126.0	106.0	113.0					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		
IRS4	8471	hgsc.bcm.edu	37	X	107979263	107979263	+	Silent	SNP	G	G	A			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											64.0	55.0	58.0					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	
SPANXN2	494119	hgsc.bcm.edu	37	X	142795459	142795459	+	Silent	SNP	G	G	T			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											298.0	267.0	278.0					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	
HCFC1	3054	hgsc.bcm.edu	37	X	153220360	153220360	+	Missense_Mutation	SNP	A	A	G	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	9.0	13.0	12.0		3490	-0.3	0.0	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	
ZNF518B	85460	hgsc.bcm.edu	37	4	10447326	10447326	+	Silent	SNP	C	C	A			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											175.0	180.0	178.0					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	
SPINK2	6691	hgsc.bcm.edu	37	4	57677869	57677869	+	Missense_Mutation	SNP	G	G	T	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											135.0	131.0	132.0					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	
DSPP	1834	hgsc.bcm.edu	37	4	88537306	88537306	+	Silent	SNP	T	T	C	rs537399785|rs374381786	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.chr4:88537306T>C	ENST00000282478.7	+	4	3525	c.3492T>C	c.(3490-3492)gaT>gaC	p.D1164D	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_Silent_p.D1164D			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1164	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)		acagcagcgatagcagcgaca	0.557																																																	0			4											42.0	57.0	52.0					4																	88537306		1574	2772	4346	88756330	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.3492T>C	4.37:g.88537306T>C			88756330	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	
ABCG2	9429	hgsc.bcm.edu	37	4	89039396	89039396	+	Nonsense_Mutation	SNP	G	G	A	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	0.0	5008	,	,		20066	0.0		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	127.0	113.0	118.0		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	
FBXW7	55294	hgsc.bcm.edu	37	4	153244185	153244185	+	Nonsense_Mutation	SNP	G	G	A	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											167.0	164.0	165.0					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		
DCHS2	54798	hgsc.bcm.edu	37	4	155156377	155156377	+	Missense_Mutation	SNP	A	A	G			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											82.0	73.0	76.0					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	
TUBB7P	56604	hgsc.bcm.edu	37	4	190905976	190905976	+	IGR	SNP	G	G	C	rs76536163	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.chr4:190905976G>C								FRG1 (21617 upstream) : RNA5SP174 (30316 downstream)																							CAACCTTGGCGCCGATCTGGT	0.711																																																	0			4											6.0	8.0	7.0					4																	190905976		2077	4108	6185	191142970	SO:0001628	intergenic_variant	56604																															4.37:g.190905976G>C			191142970		Missense_Mutation	SNP		37																																																																																				0	0.711								
TPO	7173	hgsc.bcm.edu	37	2	1497656	1497656	+	Missense_Mutation	SNP	C	C	A	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											71.0	66.0	68.0					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	
ZNF513	130557	hgsc.bcm.edu	37	2	27601843	27601843	+	Missense_Mutation	SNP	G	G	A	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	0.0008	0.0	5008	,	,		13575	0.0		0.001	False		,,,				2504	0.001																0			2						G	VAL/ALA,VAL/ALA	2,4294		0,2,2146	16.0	19.0	18.0		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	
EHD3	30845	hgsc.bcm.edu	37	2	31483747	31483747	+	Missense_Mutation	SNP	C	C	T			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											62.0	66.0	65.0					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	
LTBP1	4052	hgsc.bcm.edu	37	2	33588553	33588553	+	Missense_Mutation	SNP	C	C	T	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											173.0	161.0	165.0					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	
TCF7L1	83439	hgsc.bcm.edu	37	2	85536328	85536328	+	Missense_Mutation	SNP	T	T	C			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											48.0	52.0	50.0					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	
CYP27C1	339761	hgsc.bcm.edu	37	2	127950851	127950851	+	Missense_Mutation	SNP	T	T	G			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											80.0	76.0	77.0					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	
RAB3GAP1	22930	hgsc.bcm.edu	37	2	135884178	135884178	+	Missense_Mutation	SNP	C	C	T			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											228.0	222.0	224.0					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	
ACVR1	90	hgsc.bcm.edu	37	2	158626989	158626989	+	Missense_Mutation	SNP	C	C	A			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											131.0	103.0	113.0					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	
TTN	7273	hgsc.bcm.edu	37	2	179407928	179407928	+	Missense_Mutation	SNP	T	T	C			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											230.0	220.0	223.0					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	
TTN	7273	hgsc.bcm.edu	37	2	179482201	179482201	+	Missense_Mutation	SNP	G	G	T			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											71.0	64.0	66.0					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	
FSIP2	401024	hgsc.bcm.edu	37	2	186671833	186671833	+	Missense_Mutation	SNP	A	A	T			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											85.0	84.0	84.0					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	
DNAH7	56171	hgsc.bcm.edu	37	2	196913042	196913042	+	Missense_Mutation	SNP	A	A	T			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											123.0	113.0	116.0					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	
SGOL2	151246	hgsc.bcm.edu	37	2	201440162	201440162	+	Missense_Mutation	SNP	T	T	G			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											88.0	84.0	85.0					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	
USP37	57695	hgsc.bcm.edu	37	2	219330870	219330870	+	Missense_Mutation	SNP	C	C	A			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											136.0	132.0	133.0					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	
CHPF	79586	hgsc.bcm.edu	37	2	220404219	220404219	+	Silent	SNP	C	C	T	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	0.0008	0.0014	5008	,	,		17369	0.0		0.0	False		,,,				2504	0.0																0			2						C	,	8,4396	14.3+/-33.2	0,8,2194	46.0	41.0	43.0		1728,2214	-9.1	0.0	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	
COL4A3	1285	hgsc.bcm.edu	37	2	228128656	228128656	+	Silent	SNP	G	G	A	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	61.0	65.0	64.0		1311	0.8	1.0	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	
GLDC	2731	hgsc.bcm.edu	37	9	6558671	6558671	+	Missense_Mutation	SNP	G	G	A	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	0.0014	5008	,	,		20942	0.0		0.0	False		,,,				2504	0.0																0			9						G	LEU/PRO	0,4406		0,0,2203	112.0	100.0	104.0		1940	5.9	1.0	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	
NPR2	4882	hgsc.bcm.edu	37	9	35801945	35801945	+	Missense_Mutation	SNP	T	T	C			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											145.0	130.0	135.0					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		
GNE	10020	hgsc.bcm.edu	37	9	36246115	36246115	+	Missense_Mutation	SNP	G	G	A	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	0.0	5008	,	,		23136	0.0		0.0	False		,,,				2504	0.0				GBM(184;106 2118 20004 35750 50727)												0			9											172.0	140.0	151.0					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	
DAPK1	1612	hgsc.bcm.edu	37	9	90301542	90301542	+	Silent	SNP	G	G	A	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	80.0	95.0	90.0		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	
BICD2	23299	hgsc.bcm.edu	37	9	95484999	95484999	+	Missense_Mutation	SNP	G	G	A			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											133.0	114.0	120.0					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	
WNK2	65268	hgsc.bcm.edu	37	9	96021423	96021423	+	Missense_Mutation	SNP	C	C	T	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	0.0008	0.17	5008	,	,		9409	0.0456		0.0338	False		,,,				2504	0.002																0			9						T	SER/PRO	32,4362		0,32,2165	15.0	18.0	17.0		2593	-10.2	0.0	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	
GABBR2	9568	hgsc.bcm.edu	37	9	101073478	101073478	+	Missense_Mutation	SNP	C	C	G			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											98.0	79.0	85.0					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		
GARNL3	84253	hgsc.bcm.edu	37	9	130075823	130075823	+	Silent	SNP	T	T	C			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											173.0	157.0	162.0					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	
NBEA	26960	hgsc.bcm.edu	37	13	36223948	36223948	+	Nonsense_Mutation	SNP	C	C	T			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											103.0	103.0	103.0					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	
CHAMP1	283489	hgsc.bcm.edu	37	13	115090225	115090225	+	Missense_Mutation	SNP	C	C	T			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											47.0	53.0	51.0					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	
PLXDC2	84898	hgsc.bcm.edu	37	10	20357162	20357162	+	Missense_Mutation	SNP	A	A	G			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											81.0	76.0	77.0					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	
GPRIN2	9721	hgsc.bcm.edu	37	10	46999030	46999030	+	Silent	SNP	C	C	T	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											29.0	37.0	35.0					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	
MAPK8	5599	hgsc.bcm.edu	37	10	49628294	49628294	+	Missense_Mutation	SNP	A	A	G			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											153.0	144.0	147.0					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		
WDFY4	57705	hgsc.bcm.edu	37	10	50025396	50025396	+	Missense_Mutation	SNP	G	G	A	rs7097397	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.chr10:50025396G>A	ENST00000325239.5	+	31	5474	c.5447G>A	c.(5446-5448)cGa>cAa	p.R1816Q	WDFY4_ENST00000413659.2_3'UTR	NM_020945.1	NP_065996.1	Q6ZS81	WDFY4_HUMAN	WDFY family member 4	1816						integral component of membrane (GO:0016021)				NS(2)|breast(5)|central_nervous_system(4)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|lung(3)|pancreas(2)|prostate(5)|skin(6)|stomach(1)	48						CCAGCGTGGCGAGCCCCGGAG	0.652													G|||	1796	0.358626	0.0983	0.3271	5008	,	,		16868	0.6935		0.3956	False		,,,				2504	0.3497																0			10						G	GLN/ARG	179,1205		10,159,523	32.0	41.0	39.0	http://www.ncbi.nlm.nih.gov/pubmed?term	5447	3.6	0.8	10	dbSNP_116	39	1238,1944		239,760,592	yes	missense	WDFY4	NM_020945.1	43	249,919,1115	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	38.9063,12.9335,31.0337	possibly-damaging	1816/3185	50025396	1417,3149	692	1591	2283	49695402	SO:0001583	missense	57705			AK074085	CCDS44385.1	10q11.23	2013-01-10			ENSG00000128815	ENSG00000128815		"""WD repeat domain containing"""	29323	protein-coding gene	gene with protein product		613316	"""chromosome 10 open reading frame 64"""	C10orf64		10997877	Standard	NM_020945		Approved	KIAA1607, Em:AC060234.3, FLJ45748	uc001jha.4	Q6ZS81	OTTHUMG00000018180	ENST00000325239.5:c.5447G>A	10.37:g.50025396G>A	ENSP00000320563:p.Arg1816Gln		49695402	B9ZVP2|Q86WZ4|Q8N4A3|Q8TEN7|Q96BE1|Q9H7H8|Q9HCG5	Missense_Mutation	SNP	ENST00000325239.5	37	CCDS44385.1	856	0.39194139194139194	47	0.09552845528455285	133	0.3674033149171271	381	0.666083916083916	295	0.3891820580474934	G	8.367	0.834530	0.16820	0.129335	0.389063	ENSG00000128815	ENST00000426033;ENST00000325239	T	0.55234	0.53	5.45	3.56	0.40772	.	0.754896	0.12068	N	0.502486	T	0.00012	0.0000	M	0.65975	2.015	0.80722	P	0.0	D;P	0.53151	0.958;0.824	B;B	0.40702	0.338;0.084	T	0.45877	-0.9231	8	.	.	.	.	4.1163	0.10083	0.2661:0.0:0.5721:0.1618	rs7097397;rs17772075;rs52813133;rs7097397	344;1816	F2Z372;Q6ZS81	.;WDFY4_HUMAN	Q	1816	ENSP00000320563:R1816Q	.	R	+	2	0	WDFY4	49695402	0.001000	0.12720	0.804000	0.32291	0.383000	0.30230	1.117000	0.31234	0.642000	0.30620	-0.136000	0.14681	CGA		0.652	WDFY4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_033379	
CCDC6	8030	hgsc.bcm.edu	37	10	61552765	61552765	+	Silent	SNP	A	A	G			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											151.0	141.0	145.0					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	
CHUK	1147	hgsc.bcm.edu	37	10	101980420	101980420	+	Silent	SNP	T	T	C			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											79.0	78.0	78.0					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	
PSD	5662	hgsc.bcm.edu	37	10	104176584	104176584	+	Missense_Mutation	SNP	C	C	T			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											39.0	43.0	42.0					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		
GSTO1	9446	hgsc.bcm.edu	37	10	106022834	106022834	+	Splice_Site	SNP	A	A	T	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						72.0	67.0	69.0					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
EBF3	253738	hgsc.bcm.edu	37	10	131639129	131639129	+	Missense_Mutation	SNP	A	A	G			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											107.0	105.0	106.0					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	
NKX6-2	84504	hgsc.bcm.edu	37	10	134598560	134598560	+	Missense_Mutation	SNP	C	C	T			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											86.0	63.0	70.0					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		
PIK3R1	5295	hgsc.bcm.edu	37	5	67589614	67589614	+	Silent	SNP	A	A	G			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											45.0	49.0	48.0					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	
NAIP	4671	hgsc.bcm.edu	37	5	70308329	70308329	+	Silent	SNP	G	G	A			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											213.0	174.0	187.0					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	
ERAP1	51752	hgsc.bcm.edu	37	5	96130819	96130819	+	Missense_Mutation	SNP	G	G	A			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											76.0	70.0	72.0					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	
APC	324	hgsc.bcm.edu	37	5	112174633	112174633	+	Silent	SNP	A	A	G			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											90.0	82.0	85.0					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	
APC	324	hgsc.bcm.edu	37	5	112175271	112175271	+	Nonsense_Mutation	SNP	C	C	A			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											61.0	64.0	63.0					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	
PCDHB3	56132	hgsc.bcm.edu	37	5	140480582	140480582	+	Missense_Mutation	SNP	G	G	A	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	81.0	84.0	83.0		349	-6.6	0.0	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	
PCDHB16	57717	hgsc.bcm.edu	37	5	140564370	140564370	+	Missense_Mutation	SNP	T	T	C			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											95.0	100.0	98.0					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	
PCDHGA8	9708	hgsc.bcm.edu	37	5	140774316	140774316	+	Missense_Mutation	SNP	G	G	A			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											29.0	36.0	34.0					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	
MAPK9	5601	hgsc.bcm.edu	37	5	179696366	179696366	+	Missense_Mutation	SNP	T	T	C			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											108.0	99.0	102.0					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		
PON3	5446	hgsc.bcm.edu	37	7	95001483	95001483	+	Splice_Site	SNP	A	A	G			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											123.0	119.0	120.0					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
MFSD12	126321	hgsc.bcm.edu	37	19	3547269	3547269	+	Splice_Site	SNP	C	C	T			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											62.0	66.0	64.0					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
BLK	640	hgsc.bcm.edu	37	8	11420487	11420487	+	Splice_Site	SNP	G	G	A			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											67.0	59.0	62.0					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
SERINC2	347735	hgsc.bcm.edu	37	1	31905889	31905890	+	In_Frame_Ins	INS	-	-	CAG	rs33956499|rs3050461|rs5773362	byFrequency	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.chr1:31905889_31905890insCAG	ENST00000373709.3	+	9	1239_1240	c.1089_1090insCAG	c.(1090-1092)cag>CAGcag	p.364_364Q>QQ	SERINC2_ENST00000373710.1_In_Frame_Ins_p.373_373Q>QQ|SERINC2_ENST00000491976.1_3'UTR|SERINC2_ENST00000536859.1_In_Frame_Ins_p.368_368Q>QQ|SERINC2_ENST00000536384.1_In_Frame_Ins_p.368_368Q>QQ	NM_178865.4	NP_849196.2	Q96SA4	SERC2_HUMAN	serine incorporator 2	364					phosphatidylserine metabolic process (GO:0006658)|positive regulation of transferase activity (GO:0051347)|sphingolipid metabolic process (GO:0006665)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	L-serine transmembrane transporter activity (GO:0015194)			cervix(1)|endometrium(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(2)	12		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|all_neural(195;0.0629)|Breast(348;0.0707)|Medulloblastoma(700;0.123)		STAD - Stomach adenocarcinoma(196;0.0541)|READ - Rectum adenocarcinoma(331;0.151)		TAGACGCCACACAGCAGCAGCA	0.634														3701	0.739018	0.7617	0.7363	5008	,	,		17436	0.63		0.8598	False		,,,				2504	0.6984																0			1																																								31678477	SO:0001652	inframe_insertion	347735			AY094595	CCDS30662.1, CCDS55583.1, CCDS55584.1, CCDS55585.1	1p35.1	2008-02-05	2005-11-01	2005-11-01	ENSG00000168528	ENSG00000168528			23231	protein-coding gene	gene with protein product		614549	"""tumor differentially expressed 2-like"""	TDE2L		12949800	Standard	NM_178865		Approved	FKSG84, PRO0899, TDE2	uc010ogh.2	Q96SA4	OTTHUMG00000003796	ENST00000373709.3:c.1102_1104dupCAG	1.37:g.31905896_31905898dupCAG	ENSP00000362813:p.Gln368dup		31678476	A0AVB4|B4DJK5|B7Z567|B7ZAP2|E7EUZ9|Q86Y23	In_Frame_Ins	INS	ENST00000373709.3	37	CCDS30662.1																																																																																				0.634	SERINC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010680.1	NM_018565	
SNX7	51375	hgsc.bcm.edu	37	1	99161077	99161078	+	Frame_Shift_Del	DEL	CT	CT	-			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		
OBSCN	84033	hgsc.bcm.edu	37	1	228495932	228495933	+	Frame_Shift_Ins	INS	-	-	C	rs551717131		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.chr1:228495932_228495933insC	ENST00000422127.1	+	47	12631_12632	c.12587_12588insC	c.(12586-12591)ggcctgfs	p.L4197fs	OBSCN_ENST00000570156.2_Frame_Shift_Ins_p.L5154fs|OBSCN_ENST00000366709.4_Frame_Shift_Ins_p.L1316fs|OBSCN_ENST00000284548.11_Frame_Shift_Ins_p.L4197fs|OBSCN_ENST00000366707.4_Frame_Shift_Ins_p.L1831fs	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	4197	Ig-like 43.				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)				TGCCTACAGGGCCTGCCACTGC	0.653																																																	0			1																																								226562556	SO:0001589	frameshift_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.12589dupC	1.37:g.228495934_228495934dupC	ENSP00000409493:p.Leu4197fs		226562555	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Frame_Shift_Ins	INS	ENST00000422127.1	37	CCDS58065.1																																																																																				0.653	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
TNFAIP6	7130	hgsc.bcm.edu	37	2	152236046	152236046	+	Stop_Codon_Del	DEL	A	A	-	rs71403164|rs35060021	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.chr2:152236046delA	ENST00000243347.3	+	0	908					NM_007115.3	NP_009046.2	P98066	TSG6_HUMAN	tumor necrosis factor, alpha-induced protein 6						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)	AGCCACTTATAAAAAAAAAAA	0.289													|||unknown(HR)	2457	0.490615	0.4425	0.4207	5008	,	,		15615	0.5208		0.5189	False		,,,				2504	0.545																0			2											20.0	21.0	21.0					2																	152236046		2160	4277	6437	151944292	SO:0001567	stop_retained_variant	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	Exception_encountered	2.37:g.152236046delA			151944292	Q53TI7|Q8WWI9	Frame_Shift_Del	DEL	ENST00000243347.3	37	CCDS2193.1																																																																																				0.289	TNFAIP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254834.2	NM_007115	
MUC4	4585	hgsc.bcm.edu	37	3	195515367	195515414	+	In_Frame_Del	DEL	GGTGACAGGAAGAGGGGTGGTGTGACCTGTGGATACTGAGGAAGGGCT	GGTGACAGGAAGAGGGGTGGTGTGACCTGTGGATACTGAGGAAGGGCT	-	rs369312980|rs547775645|rs201510137|rs200193644|rs531942134|rs13060431|rs200400545|rs71180964|rs199583597|rs55868431|rs55803325|rs550428312|rs199702053|rs13065584	byFrequency	TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	GGTGACAGGAAGAGGGGTGGTGTGACCTGTGGATACTGAGGAAGGGCT	GGTGACAGGAAGAGGGGTGGTGTGACCTGTGGATACTGAGGAAGGGCT					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr3:195515367_195515414delGGTGACAGGAAGAGGGGTGGTGTGACCTGTGGATACTGAGGAAGGGCT	ENST00000463781.3	-	2	3496_3543	c.3037_3084delAGCCCTTCCTCAGTATCCACAGGTCACACCACCCCTCTTCCTGTCACC	c.(3037-3084)agcccttcctcagtatccacaggtcacaccacccctcttcctgtcaccdel	p.SPSSVSTGHTTPLPVT1013del	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_In_Frame_Del_p.SPSSVSTGHTTPLPVT1013del|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	448	Repeat.|Ser-rich.				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.S1013_T1028delSPSSVSTGHTTPLPVT(4)|p.S1013G(2)|p.T1022A(2)		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)		AGGAAGTGTCGGTGACAGGAAGAGGGGTGGTGTGACCTGTGGATACTGAGGAAGGGCTGGTGACAGGA	0.573																																																	8	Substitution - Missense(4)|Deletion - In frame(4)	stomach(6)|prostate(2)	3																																								196999809	SO:0001651	inframe_deletion	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	ENST00000463781.3:c.3037_3084delAGCCCTTCCTCAGTATCCACAGGTCACACCACCCCTCTTCCTGTCACC	3.37:g.195515367_195515414delGGTGACAGGAAGAGGGGTGGTGTGACCTGTGGATACTGAGGAAGGGCT	ENSP00000417498:p.Ser1013_Thr1028del		196999762	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	In_Frame_Del	DEL	ENST00000463781.3	37	CCDS54700.1																																																																																				0.573	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
ADAM29	11086	hgsc.bcm.edu	37	4	175899072	175899098	+	In_Frame_Del	DEL	TGACACCCTCCCAGAGGCAACCTCAGT	TGACACCCTCCCAGAGGCAACCTCAGT	-	rs140568401|rs141115697|rs61744599|rs137958266|rs538790099|rs199709256|rs146933346|rs151310201	byFrequency	TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	TGACACCCTCCCAGAGGCAACCTCAGT	TGACACCCTCCCAGAGGCAACCTCAGT					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr4:175899072_175899098delTGACACCCTCCCAGAGGCAACCTCAGT	ENST00000359240.3	+	5	3066_3092	c.2396_2422delTGACACCCTCCCAGAGGCAACCTCAGT	c.(2395-2424)gtgacaccctcccagaggcaacctcagttg>gtg	p.TPSQRQPQL800del	ADAM29_ENST00000514159.1_In_Frame_Del_p.TPSQRQPQL800del|ADAM29_ENST00000445694.1_In_Frame_Del_p.TPSQRQPQL800del|ADAM29_ENST00000404450.4_In_Frame_Del_p.TPSQRQPQL800del|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	800	9 X 9 AA approximate repeats.				spermatogenesis (GO:0007283)	integral component of plasma membrane (GO:0005887)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.Q803*(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)		CAACCTCCTGTGACACCCTCCCAGAGGCAACCTCAGTTGATGCCTTC	0.577																																					Ovarian(140;1727 1835 21805 25838 41440)												1	Substitution - Nonsense(1)	lung(1)	4																																								176135673	SO:0001651	inframe_deletion	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.2396_2422delTGACACCCTCCCAGAGGCAACCTCAGT	4.37:g.175899072_175899098delTGACACCCTCCCAGAGGCAACCTCAGT	ENSP00000352177:p.Thr800_Leu808del		176135647	Q4W5F3|Q9UHP1|Q9UKF3|Q9UKF4	In_Frame_Del	DEL	ENST00000359240.3	37	CCDS3823.1																																																																																				0.577	ADAM29-201	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding			
TSPYL1	7259	hgsc.bcm.edu	37	6	116600465	116600466	+	In_Frame_Ins	INS	-	-	CAC	rs76746450|rs397735194|rs78371471|rs56100880	byFrequency	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.chr6:116600465_116600466insCAC	ENST00000368608.3	-	1	600_601	c.528_529insGTG	c.(526-531)gtgaag>gtgGTGaag	p.176_177insV	RP1-93H18.1_ENST00000449314.1_lincRNA|DSE_ENST00000540275.1_Intron|DSE_ENST00000452085.3_5'Flank	NM_003309.3	NP_003300.1	Q9H0U9	TSYL1_HUMAN	TSPY-like 1	176					nucleosome assembly (GO:0006334)	nucleus (GO:0005634)	enzyme binding (GO:0019899)	p.V176_K177insV(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)		aggccttccttcaccacctcAG	0.614														4368	0.872204	0.9592	0.7839	5008	,	,		18686	0.9772		0.6521	False		,,,				2504	0.9356																1	Insertion - In frame(1)	ovary(1)	6								3880,384		1772,336,24						-8.3	0.0		dbSNP_131	62	5244,3010		1653,1938,536	no	coding	TSPYL1	NM_003309.3		3425,2274,560	A1A1,A1R,RR		36.4672,9.0056,27.113				9124,3394				116707159	SO:0001652	inframe_insertion	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.526_528dupGTG	6.37:g.116600469_116600471dupCAC	ENSP00000357597:p.Val176_Val176dup		116707158	O75885|Q5TFE6	In_Frame_Ins	INS	ENST00000368608.3	37	CCDS34518.1																																																																																				0.614	TSPYL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041929.1		
Unknown	0	hgsc.bcm.edu	37	Unknown	0	0	+	IGR	INS	-	-	C			TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	-	-					Unknown	Invalid:failed_liftOver	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chrUnknown:0_0insC								None (None upstream) : None (None downstream)																								0.0																																																	0			7																																								6160040	SO:0001628	intergenic_variant	84132																															Unknown.37:g.0_0insC			6160039		Frame_Shift_Ins	INS		37																																																																																				0	0								
DDHD2	23259	hgsc.bcm.edu	37	8	38109742	38109747	+	In_Frame_Del	DEL	AAAAAG	AAAAAG	-			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	
GPRIN2	9721	hgsc.bcm.edu	37	10	46999591	46999592	+	In_Frame_Ins	INS	-	-	ATGAGGGAG	rs112620425	byFrequency	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.chr10:46999591_46999592insATGAGGGAG	ENST00000374317.1	+	3	984_985	c.711_712insATGAGGGAG	c.(712-714)atg>ATGAGGGAGatg	p.238_238M>MREM	GPRIN2_ENST00000374314.4_In_Frame_Ins_p.238_238M>MREM	NM_014696.3	NP_055511.2	O60269	GRIN2_HUMAN	G protein regulated inducer of neurite outgrowth 2	238								p.G237_M238insMRE(1)		breast(2)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)	18						TACTCTGTGGCATGAGGGAGGT	0.629														2399	0.479034	0.4697	0.4856	5008	,	,		38874	0.4782		0.4761	False		,,,				2504	0.4908																1	Insertion - In frame(1)	breast(1)	10								2080,27,2157		11,3,2055,0,24,39						0.9	0.0		dbSNP_130	49	3974,98,4180		16,7,3935,0,91,77	no	codingComplex	GPRIN2	NM_014696.3		27,10,5990,0,115,116	A1A1,A1A2,A1R,A2A2,A2R,RR		49.3456,49.4137,49.3688				6054,125,6337				46419598	SO:0001652	inframe_insertion	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.712_720dupATGAGGGAG	10.37:g.46999592_46999600dupATGAGGGAG	Exception_encountered		46419597	Q5SVF0	In_Frame_Ins	INS	ENST00000374317.1	37	CCDS31192.1																																																																																				0.629	GPRIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047836.1	NM_014696	
TMBIM4	51643	hgsc.bcm.edu	37	12	66531937	66531937	+	Frame_Shift_Del	DEL	A	A	-	rs199863727	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.chr12:66531937delA	ENST00000358230.3	-	7	640	c.520delT	c.(520-522)tatfs	p.Y174fs	TMBIM4_ENST00000542724.1_Frame_Shift_Del_p.Y143fs|TMBIM4_ENST00000544599.1_5'UTR|TMBIM4_ENST00000556010.1_Intron|TMBIM4_ENST00000398033.4_Frame_Shift_Del_p.F158fs|TMBIM4_ENST00000286424.7_Frame_Shift_Del_p.Y221fs|TMBIM4_ENST00000539652.1_Intron	NM_016056.2	NP_057140.2	Q9HC24	LFG4_HUMAN	transmembrane BAX inhibitor motif containing 4	174					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)				central_nervous_system(1)|endometrium(1)|large_intestine(4)|ovary(1)|prostate(2)	9				GBM - Glioblastoma multiforme(28;0.0745)		ATCTCACTATAAAAAAAAAAC	0.353																																																	0			12								30,27,3421		0,0,30,0,27,1682	40.0	38.0	38.0			6.2	0.1	12		41	61,77,7666		0,0,61,0,77,3764	no	codingComplex	TMBIM4	NM_016056.2		0,0,91,0,104,5446	A1A1,A1A2,A1R,A2A2,A2R,RR		1.7683,1.6389,1.7284			66531937	91,104,11087	1806	4076	5882	64818204	SO:0001589	frameshift_variant	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.520delT	12.37:g.66531937delA	ENSP00000350965:p.Tyr174fs		64818204	Q542Z6|Q9UHY5|Q9Y3C2	Frame_Shift_Del	DEL	ENST00000358230.3	37	CCDS41805.1																																																																																				0.353	TMBIM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401832.2	NM_016056	
C14orf177	283598	hgsc.bcm.edu	37	14	99182527	99182535	+	Start_Codon_Del	DEL	GGATGCATC	GGATGCATC	-	rs17097718|rs373583218|rs139827156	byFrequency	TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	GGATGCATC	GGATGCATC					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr14:99182527_99182535delGGATGCATC	ENST00000325812.2	+	0	418_426					NM_182560.2	NP_872366.2	Q52M58	CN177_HUMAN	chromosome 14 open reading frame 177											endometrium(1)|kidney(1)|large_intestine(1)|lung(10)	13		Melanoma(154;0.128)				CAGTACGACTGGATGCATCGGAAAGAGCC	0.569														134	0.0267572	0.0356	0.0245	5008	,	,		21205	0.004		0.0567	False		,,,				2504	0.0092																0			14								127,4135		2,123,2006						1.8	0.0		dbSNP_134	53	465,7787		31,403,3692	no	coding	C14orf177	NM_182560.2		33,526,5698	A1A1,A1R,RR		5.635,2.9798,4.7307				592,11922				98252288	SO:0001582	initiator_codon_variant	283598			AK098639	CCDS9948.1	14q32.2	2012-05-30			ENSG00000176605	ENSG00000176605			26375	protein-coding gene	gene with protein product						12477932	Standard	NM_182560		Approved	FLJ25773	uc001yfz.2	Q52M58	OTTHUMG00000167745		14.37:g.99182527_99182535delGGATGCATC			98252280	Q8N7D2	Frame_Shift_Del	DEL	ENST00000325812.2	37	CCDS9948.1																																																																																				0.569	C14orf177-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396078.1	NM_182560	
ZFYVE19	84936	hgsc.bcm.edu	37	15	41099899	41099900	+	Frame_Shift_Ins	INS	-	-	GGGGC	rs371684343|rs200042011|rs142730574|rs369585041	byFrequency	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.chr15:41099899_41099900insGGGGC	ENST00000355341.4	+	1	613_614	c.112_113insGGGGC	c.(112-114)tggfs	p.-40fs	ZFYVE19_ENST00000336455.5_Intron|ZFYVE19_ENST00000563530.1_3'UTR|DNAJC17_ENST00000220496.4_5'Flank|ZFYVE19_ENST00000564258.1_Intron|ZFYVE19_ENST00000299173.10_Frame_Shift_Ins_p.-40fs|ZFYVE19_ENST00000570108.1_Intron	NM_001077268.1	NP_001070736.1	Q96K21	ANCHR_HUMAN	zinc finger, FYVE domain containing 19						abscission (GO:0009838)|cell division (GO:0051301)|cytokinesis checkpoint (GO:0031565)|negative regulation of cytokinesis (GO:0032466)	centrosome (GO:0005813)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|midbody (GO:0030496)	phosphatidylinositol-3-phosphate binding (GO:0032266)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	9		all_cancers(109;3.31e-18)|all_epithelial(112;2.33e-15)|Lung NSC(122;5.34e-11)|all_lung(180;1.33e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;2.76e-05)|COAD - Colon adenocarcinoma(120;0.151)|BRCA - Breast invasive adenocarcinoma(123;0.164)		AGTGGGCGTGTGgggcggggca	0.718														1685	0.336462	0.3411	0.3112	5008	,	,		13821	0.2252		0.3777	False		,,,				2504	0.4202																0			15								1226,2460		247,732,864						2.0	0.3		dbSNP_130	17	2598,5206		494,1610,1798	no	frameshift	ZFYVE19	NM_001077268.1		741,2342,2662	A1A1,A1R,RR		33.2906,33.261,33.2811				3824,7666				38887192	SO:0001589	frameshift_variant	84936			AK027746	CCDS42025.1, CCDS58353.1, CCDS58354.1, CCDS58355.1	15q14	2008-05-02				ENSG00000166140		"""Zinc fingers, FYVE domain containing"""	20758	protein-coding gene	gene with protein product							Standard	NM_001077268		Approved	FLJ14840	uc031qrk.1	Q96K21		ENST00000355341.4:c.118_122dupGGGGC	15.37:g.41099905_41099909dupGGGGC	ENSP00000347498:p.Gly40fs		38887191	B3KVB2|C9JNF4|H3BUF9|Q86WC2|Q8WU96	Frame_Shift_Ins	INS	ENST00000355341.4	37	CCDS42025.1																																																																																				0.718	ZFYVE19-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418996.1	NM_032850	
SYNM	23336	hgsc.bcm.edu	37	15	99646107	99646108	+	Splice_Site	INS	-	-	G	rs67855410|rs200549249|rs60530833		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.chr15:99646107_99646108insG	ENST00000336292.6	+	1	822	c.702_702insG	c.(703-705)gcg>gcGg	p.A235fs	SYNM_ENST00000561323.1_3'UTR|SYNM_ENST00000560674.1_Intron|RP11-654A16.3_ENST00000559468.1_RNA|SYNM_ENST00000328642.7_Splice_Site_p.A235fs	NM_145728.2	NP_663780.2	O15061	SYNEM_HUMAN	synemin, intermediate filament protein	236	Coil 2.|Interaction with DMD and UTRN.|Rod.				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						CGCAGGAGGCAAGGCGCTGCGG	0.728													G|-|G|deletion	5008	1.0	1.0	1.0	5008	,	,		10929	1.0		1.0	False		,,,				2504	1.0				Pancreas(125;1071 1762 21750 40003 40381)												0			15							,	3381,17		1690,1,8					,	-8.2	0.6		dbSNP_130	4	6685,35		3338,9,13	no	frameshift,frameshift	SYNM	NM_145728.2,NM_015286.5	,	5028,10,21	A1A1,A1R,RR		0.5208,0.5003,0.5139	,	,		10066,52				97463631	SO:0001630	splice_region_variant	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.702+1->G	15.37:g.99646107_99646108insG			97463630	A7E2Y2|Q2TBJ4|Q5NJJ9|Q8TE61|Q8TE62	Frame_Shift_Ins	INS	ENST00000336292.6	37																																																																																					0.728	SYNM-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_145728	Frame_Shift_Ins
KRTAP4-1	85285	hgsc.bcm.edu	37	17	39340796	39340852	+	In_Frame_Del	DEL	CGGCAGCAGCTGGACATACCACAGCTGGGGTGGCAGGTGGTCTGACAGCAGAGTGGG	CGGCAGCAGCTGGACATACCACAGCTGGGGTGGCAGGTGGTCTGACAGCAGAGTGGG	-	rs483929|rs543483191|rs79048996|rs1985673|rs2320229|rs483893|rs572749|rs543006020|rs71155126|rs554407371|rs2320230	byFrequency	TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	CGGCAGCAGCTGGACATACCACAGCTGGGGTGGCAGGTGGTCTGACAGCAGAGTGGG	CGGCAGCAGCTGGACATACCACAGCTGGGGTGGCAGGTGGTCTGACAGCAGAGTGGG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr17:39340796_39340852delCGGCAGCAGCTGGACATACCACAGCTGGGGTGGCAGGTGGTCTGACAGCAGAGTGGG	ENST00000398472.1	-	1	742_798	c.255_311delCCCACTCTGCTGTCAGACCACCTGCCACCCCAGCTGTGGTATGTCCAGCTGCTGCCG	c.(253-312)cgcccactctgctgtcagaccacctgccaccccagctgtggtatgtccagctgctgccgt>cgt	p.85_104RPLCCQTTCHPSCGMSSCCR>R				Q9BYQ7	KRA41_HUMAN	keratin associated protein 4-1	85	18 X 5 AA repeats of C-C-[GRQC]-[SPT]- [VSTL].		Missing (in allele KAP4.10). {ECO:0000269|PubMed:15955084}.			keratin filament (GO:0045095)		p.H90_C108delHPSCGMSSCCRPLCCQTTC(2)|p.H94_C112delHPSCGMSSCCRPLCCQTTC(2)		kidney(1)|large_intestine(1)|lung(1)|prostate(1)|upper_aerodigestive_tract(1)	5		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000449)			ACAGAGTGGACGGCAGCAGCTGGACATACCACAGCTGGGGTGGCAGGTGGTCTGACAGCAGAGTGGGCGGCAGCAGC	0.646																																																	4	Deletion - In frame(4)	upper_aerodigestive_tract(2)|prostate(2)	17																																								36594378	SO:0001651	inframe_deletion	85285			AC006070		17q21.2	2013-06-25			ENSG00000198443	ENSG00000198443		"""Keratin associated proteins"""	18907	protein-coding gene	gene with protein product			"""keratin associated protein 4-10"""	KRTAP4-10		11279113	Standard	NM_033060		Approved	KAP4.1, KAP4.10	uc002hwe.4	Q9BYQ7	OTTHUMG00000132081	ENST00000398472.1:c.255_311delCCCACTCTGCTGTCAGACCACCTGCCACCCCAGCTGTGGTATGTCCAGCTGCTGCCG	17.37:g.39340796_39340852delCGGCAGCAGCTGGACATACCACAGCTGGGGTGGCAGGTGGTCTGACAGCAGAGTGGG	ENSP00000381489:p.Arg85_Cys103del		36594322	A8MWS7|Q3SYF2	Frame_Shift_Del	DEL	ENST00000398472.1	37																																																																																					0.646	KRTAP4-1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000255108.1	NM_033060	
KRTAP9-8	83901	hgsc.bcm.edu	37	17	39394711	39394725	+	In_Frame_Del	DEL	GACCACCTGCTGCAG	GACCACCTGCTGCAG	-	rs550091794|rs374427254|rs373648251	byFrequency	TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	GACCACCTGCTGCAG	GACCACCTGCTGCAG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr17:39394711_39394725delGACCACCTGCTGCAG	ENST00000254072.6	+	1	415_429	c.408_422delGACCACCTGCTGCAG	c.(406-423)gagaccacctgctgcagg>gag	p.TTCCR137del		NM_031963.2	NP_114169.2	Q9BYQ0	KRA98_HUMAN	keratin associated protein 9-8	137	15 X 5 AA repeats of C-C-[RQVSGE]- [SPSNQ]-[TASPI].					keratin filament (GO:0045095)				lung(8)|ovary(1)|prostate(1)	10		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000397)			CCTGCTGTGAGACCACCTGCTGCAGGACCACTTGC	0.591																																																	0			17																																								36648251	SO:0001651	inframe_deletion	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.408_422delGACCACCTGCTGCAG	17.37:g.39394711_39394725delGACCACCTGCTGCAG	ENSP00000254072:p.Thr137_Arg141del		36648237		In_Frame_Del	DEL	ENST00000254072.6	37	CCDS42334.1																																																																																				0.591	KRTAP9-8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257712.1		
ZNF233	353355	hgsc.bcm.edu	37	19	44778796	44778796	+	Frame_Shift_Del	DEL	G	G	-	rs386809644|rs59660444|rs75921463|rs386809645	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.chr19:44778796delG	ENST00000391958.2	+	5	2110	c.1983delG	c.(1981-1983)tcgfs	p.S661fs	ZNF233_ENST00000592581.1_3'UTR|ZNF235_ENST00000589799.1_Intron|ZNF233_ENST00000334152.1_Frame_Shift_Del_p.S643fs	NM_181756.2	NP_861421.2	A6NK53	ZN233_HUMAN	zinc finger protein 233	661					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)|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)				GTAAGAGTTCGTTGTCTTCAG	0.418													?|G|-|unsure	1594	0.318291	0.6536	0.3372	5008	,	,		19999	0.2579		0.1322	False		,,,				2504	0.1053																0			19											39.0	73.0	61.0					19																	44778796		2094	4294	6388	49470636	SO:0001589	frameshift_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.1983delG	19.37:g.44778796delG	ENSP00000375820:p.Ser661fs		49470636	B2RN78|B2RN79|Q86WL8	Frame_Shift_Del	DEL	ENST00000391958.2	37	CCDS33047.1																																																																																				0.418	ZNF233-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000460737.1	NM_181756	
RALY	22913	hgsc.bcm.edu	37	20	32664864	32664865	+	In_Frame_Ins	INS	-	-	CAG	rs10649600|rs57852506	byFrequency	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.chr20:32664864_32664865insCAG	ENST00000246194.3	+	8	1191_1192	c.689_690insCAG	c.(688-693)gccggc>gcCAGcggc	p.230_231AG>ASG	RALY_ENST00000375114.3_In_Frame_Ins_p.214_215AG>ASG	NM_016732.2	NP_057951.1	Q9UKM9	RALY_HUMAN	RALY heterogeneous nuclear ribonucleoprotein	230	Epitope (recognized by BKRF1 antibodies).|Poly-Gly.			A -> AS (in Ref. 2; AAC28898). {ECO:0000305}.	mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			kidney(2)|large_intestine(3)|lung(2)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	12						GGAggtggcgccggcggcggcg	0.658																																																	0			20																																								32128526	SO:0001652	inframe_insertion	22913			AF148457	CCDS13229.1, CCDS13230.1	20q11.21-q11.23	2013-08-06	2013-08-06		ENSG00000125970	ENSG00000125970		"""RNA binding motif (RRM) containing"""	15921	protein-coding gene	gene with protein product		614663	"""RNA-binding protein (autoantigenic, hnRNP-associated with lethal yellow)"", ""RNA binding protein, autoantigenic (hnRNP-associated with lethal yellow homolog (mouse))"""			10500250, 23614458	Standard	NM_016732		Approved	P542, HNRPCL2	uc002xab.3	Q9UKM9	OTTHUMG00000032283	Exception_encountered	20.37:g.32664864_32664865insCAG	ENSP00000246194:p.Ala230_Gly231insSer		32128525	Q14621|Q2M365|Q5QPL8|Q9BQX6|Q9UJE3	In_Frame_Ins	INS	ENST00000246194.3	37	CCDS13230.1																																																																																				0.658	RALY-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078753.1		
C22orf39	128977	hgsc.bcm.edu	37	22	19435243	19435250	+	Frame_Shift_Del	DEL	TCAGTCCG	TCAGTCCG	-	rs200087123	byFrequency	TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	TCAGTCCG	TCAGTCCG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr22:19435243_19435250delTCAGTCCG	ENST00000399562.4	-	1	505_512	c.73_80delCGGACTGA	c.(73-81)cggactgagfs	p.RTE25fs	HIRA_ENST00000546308.1_5'Flank|AC000068.5_ENST00000431090.1_RNA|C22orf39_ENST00000399568.1_5'Flank|C22orf39_ENST00000333059.5_5'Flank|C22orf39_ENST00000542103.1_Frame_Shift_Del_p.RTE25fs|HIRA_ENST00000541063.1_5'Flank	NM_173793.4	NP_776154.3	Q6P5X5	CV039_HUMAN	chromosome 22 open reading frame 39	25												Colorectal(54;0.0993)					AGCCCGCCCCTCAGTCCGCCAGCCAATG	0.615																																																	0			22							,	26,3872		4,18,1927					,	0.4	0.0			18	49,7635		4,41,3797	no	frameshift,frameshift	C22orf39	NM_173793.4,NM_001166242.1	,	8,59,5724	A1A1,A1R,RR		0.6377,0.667,0.6476	,	,		75,11507				17815250	SO:0001589	frameshift_variant	128977				CCDS33599.1, CCDS33599.2, CCDS54498.1	22q11.21	2008-10-31			ENSG00000242259	ENSG00000242259			27012	protein-coding gene	gene with protein product							Standard	NM_173793		Approved	MGC74441	uc002zpk.2	Q6P5X5	OTTHUMG00000150137	ENST00000399562.4:c.73_80delCGGACTGA	22.37:g.19435243_19435250delTCAGTCCG	ENSP00000382474:p.Arg25fs		17815243	A8MTW6|D3DX18|F5H3A8|J3KNP9	Frame_Shift_Del	DEL	ENST00000399562.4	37	CCDS33599.2																																																																																				0.615	C22orf39-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000316494.3	NM_173793	
NEFH	4744	hgsc.bcm.edu	37	22	29885581	29885604	+	In_Frame_Del	DEL	AGGCCAAGTCCCCAGAGAAGGAAG	AGGCCAAGTCCCCAGAGAAGGAAG	-	rs267607534|rs373980795|rs267607533|rs149571560|rs79235463|rs200984527|rs370803228	byFrequency	TCGA-CL-5918-01A-11D-1657-10	TCGA-CL-5918-10A-01D-1657-10	AGGCCAAGTCCCCAGAGAAGGAAG	AGGCCAAGTCCCCAGAGAAGGAAG					Unknown	Unknown	Somatic	Phase_I	Capture	none			Illumina HiSeq	96c37a26-e65f-4fb3-813e-f1716ea6a0a3	b6d0adbc-80e8-4f85-aa89-903ff102635b	g.chr22:29885581_29885604delAGGCCAAGTCCCCAGAGAAGGAAG	ENST00000310624.6	+	4	1985_2008	c.1952_1975delAGGCCAAGTCCCCAGAGAAGGAAG	c.(1951-1977)aaggccaagtccccagagaaggaagag>aag	p.AKSPEKEE652del		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	658	30 X 6 AA repeats of K-S-P-[AEPV]-[EAK]- [AEVK].|Tail.			Missing (in Ref. 1; CAA33366 and 5; AC000035). {ECO:0000305}.	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						TCCCCTGAGAAGGCCAAGTCCCCAGAGAAGGAAGAGGCCAAGTC	0.562																																																	0			22																																								28215604	SO:0001651	inframe_deletion	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.1952_1975delAGGCCAAGTCCCCAGAGAAGGAAG	22.37:g.29885581_29885604delAGGCCAAGTCCCCAGAGAAGGAAG	ENSP00000311997:p.Ala652_Glu659del		28215581	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	In_Frame_Del	DEL	ENST00000310624.6	37	CCDS13858.1																																																																																				0.562	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076	
SHROOM4	57477	hgsc.bcm.edu	37	X	50350758	50350759	+	In_Frame_Ins	INS	-	-	TGCTGCTGCTGT	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	0.0			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	
