Atlas of Genetics and Cytogenetics in Oncology and Haematology

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CDH23 (cadherin related 23)

Identity

Alias_namesDFNB12
USH1D
cadherin-like 23
Alias_symbol (synonym)CDHR23
Other aliasPITA5
HGNC (Hugo) CDH23
LocusID (NCBI) 64072
Atlas_Id 52846
Location 10q22.1  [Link to chromosome band 10q22]
Location_base_pair Starts at 71396934 and ends at 71647462 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2017)		Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
BTRC (10q24.32) / CDH23 (10q22.1)C10orf54 (10q22.1) / CDH23 (10q22.1)CDH23 (10q22.1) / DLG2 (11q14.1)
CDH23 (10q22.1) / FAM110D (1p36.11)CDH23 (10q22.1) / NSD1 (5q35.2)CDH23 (10q22.1) / ZNF664 (12q24.31)
CHST3 (10q22.1) / CDH23 (10q22.1)KLK5 (19q13.41) / CDH23 (10q22.1)LTBP1 (2p22.3) / CDH23 (10q22.1)
NSD1 (5q35.2) / CDH23 (10q22.1)RAB13 (1q21.3) / CDH23 (10q22.1)RAB5B (12q13.2) / CDH23 (10q22.1)
SHB (9p13.2) / CDH23 (10q22.1)BTRC 10q24.32 / CDH23 10q22.1CDH23 10q22.1 / NSD1 5q35.2
CHST3 10q22.1 / CDH23 10q22.1LTBP1 2p22.3 / CDH23 10q22.1NSD1 5q35.2 / CDH23 10q22.1

Note

Non-annotated gene. Preliminary data : if you are an author
who wish to write a full paper/card on this gene, go to  How to contribute

DNA/RNA

 

Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 6 ]
  t(2;10)(p22;q22) LTBP1/CDH23
t(5;10)(q35;q22) CDH23/NSD1
t(5;10)(q35;q22) NSD1/CDH23
CHST3/CDH23 (10q22)
t(10;10)(q22;q24) BTRC/CDH23
t(10;19)(q22;q13) KLK5/CDH23

External links

Nomenclature
HGNC (Hugo)CDH23   13733
Cards
Entrez_Gene (NCBI)CDH23  64072  cadherin related 23
AliasesCDHR23; PITA5; USH1D
GeneCards (Weizmann)CDH23
Ensembl hg19 (Hinxton)ENSG00000107736 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000107736 [Gene_View]  ENSG00000107736 [Sequence]  chr10:71396934-71647462 [Contig_View]  CDH23 [Vega]
ICGC DataPortalENSG00000107736
TCGA cBioPortalCDH23
AceView (NCBI)CDH23
Genatlas (Paris)CDH23
WikiGenes64072
SOURCE (Princeton)CDH23
Genetics Home Reference (NIH)CDH23
Genomic and cartography
GoldenPath hg38 (UCSC)CDH23  -     chr10:71396934-71647462 +  10q22.1   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)CDH23  -     10q22.1   [Description]    (hg19-Feb_2009)
GoldenPathCDH23 - 10q22.1 [CytoView hg19]  CDH23 - 10q22.1 [CytoView hg38]
ImmunoBaseENSG00000107736
Mapping of homologs : NCBICDH23 [Mapview hg19]  CDH23 [Mapview hg38]
OMIM601067   601386   605516   617540   
Gene and transcription
Genbank (Entrez)AB053445 AB058715 AF312024 AK074160 AK093818
RefSeq transcript (Entrez)NM_001171930 NM_001171931 NM_001171932 NM_001171933 NM_001171934 NM_001171935 NM_001171936 NM_022124 NM_052836
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)CDH23
Cluster EST : UnigeneHs.656032 [ NCBI ]
CGAP (NCI)Hs.656032
Alternative Splicing GalleryENSG00000107736
Gene ExpressionCDH23 [ NCBI-GEO ]   CDH23 [ EBI - ARRAY_EXPRESS ]   CDH23 [ SEEK ]   CDH23 [ MEM ]
Gene Expression Viewer (FireBrowse)CDH23 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)64072
GTEX Portal (Tissue expression)CDH23
Human Protein AtlasENSG00000107736-CDH23 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ9H251   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ9H251  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ9H251
Splice isoforms : SwissVarQ9H251
PhosPhoSitePlusQ9H251
Domaine pattern : Prosite (Expaxy)CADHERIN_1 (PS00232)    CADHERIN_2 (PS50268)   
Domains : Interpro (EBI)Cadherin    Cadherin-like    Cadherin_CS    CDH23   
Domain families : Pfam (Sanger)Cadherin (PF00028)   
Domain families : Pfam (NCBI)pfam00028   
Domain families : Smart (EMBL)CA (SM00112)  
Conserved Domain (NCBI)CDH23
DMDM Disease mutations64072
Blocks (Seattle)CDH23
PDB (RSDB)2KBR    2KBS    2LSR    5TFM   
PDB Europe2KBR    2KBS    2LSR    5TFM   
PDB (PDBSum)2KBR    2KBS    2LSR    5TFM   
PDB (IMB)2KBR    2KBS    2LSR    5TFM   
Structural Biology KnowledgeBase2KBR    2KBS    2LSR    5TFM   
SCOP (Structural Classification of Proteins)2KBR    2KBS    2LSR    5TFM   
CATH (Classification of proteins structures)2KBR    2KBS    2LSR    5TFM   
SuperfamilyQ9H251
Human Protein Atlas [tissue]ENSG00000107736-CDH23 [tissue]
Peptide AtlasQ9H251
HPRD05699
IPIIPI01012113   IPI00216561   IPI00216562   IPI00827563   IPI00872875   IPI00296026   IPI00216560   IPI01019019   IPI00942477   IPI00419673   IPI00177323   IPI01018633   IPI01018993   IPI00847368   IPI00940291   IPI00955424   IPI00514211   IPI00514764   IPI00386849   
Protein Interaction databases
DIP (DOE-UCLA)Q9H251
IntAct (EBI)Q9H251
FunCoupENSG00000107736
BioGRIDCDH23
STRING (EMBL)CDH23
ZODIACCDH23
Ontologies - Pathways
QuickGOQ9H251
Ontology : AmiGOcalcium ion binding  protein binding  plasma membrane  calcium ion transport  homophilic cell adhesion via plasma membrane adhesion molecules  visual perception  sensory perception of sound  locomotory behavior  membrane  integral component of membrane  calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules  stereocilium  photoreceptor cell maintenance  response to stimulus  sensory perception of light stimulus  equilibrioception  regulation of cytosolic calcium ion concentration  inner ear receptor cell stereocilium organization  
Ontology : EGO-EBIcalcium ion binding  protein binding  plasma membrane  calcium ion transport  homophilic cell adhesion via plasma membrane adhesion molecules  visual perception  sensory perception of sound  locomotory behavior  membrane  integral component of membrane  calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules  stereocilium  photoreceptor cell maintenance  response to stimulus  sensory perception of light stimulus  equilibrioception  regulation of cytosolic calcium ion concentration  inner ear receptor cell stereocilium organization  
NDEx NetworkCDH23
Atlas of Cancer Signalling NetworkCDH23
Wikipedia pathwaysCDH23
Orthology - Evolution
OrthoDB64072
GeneTree (enSembl)ENSG00000107736
Phylogenetic Trees/Animal Genes : TreeFamCDH23
HOGENOMQ9H251
Homologs : HomoloGeneCDH23
Homology/Alignments : Family Browser (UCSC)CDH23
Gene fusions - Rearrangements
Fusion : MitelmanBTRC/CDH23 [10q24.32/10q22.1]  [t(10;10)(q22;q24)]  
Fusion : MitelmanCDH23/NSD1 [10q22.1/5q35.2]  [t(5;10)(q35;q22)]  
Fusion : MitelmanCHST3/CDH23 [10q22.1/10q22.1]  [t(10;10)(q22;q22)]  
Fusion : MitelmanKLK5/CDH23 [19q13.41/10q22.1]  [t(10;19)(q22;q13)]  
Fusion : MitelmanLTBP1/CDH23 [2p22.3/10q22.1]  [t(2;10)(p22;q22)]  
Fusion : MitelmanNSD1/CDH23 [5q35.2/10q22.1]  [t(5;10)(q35;q22)]  
Fusion PortalBTRC 10q24.32 CDH23 10q22.1 BRCA
Fusion PortalCDH23 10q22.1 NSD1 5q35.2 BRCA
Fusion PortalCHST3 10q22.1 CDH23 10q22.1 LUAD
Fusion PortalLTBP1 2p22.3 CDH23 10q22.1 BRCA
Fusion PortalNSD1 5q35.2 CDH23 10q22.1 BRCA
Fusion : QuiverCDH23
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerCDH23 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)CDH23
dbVarCDH23
ClinVarCDH23
1000_GenomesCDH23 
Exome Variant ServerCDH23
ExAC (Exome Aggregation Consortium)ENSG00000107736
GNOMAD BrowserENSG00000107736
Varsome BrowserCDH23
Genetic variants : HAPMAP64072
Genomic Variants (DGV)CDH23 [DGVbeta]
DECIPHERCDH23 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisCDH23 
Mutations
ICGC Data PortalCDH23 
TCGA Data PortalCDH23 
Broad Tumor PortalCDH23
OASIS PortalCDH23 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICCDH23  [overview]  [genome browser]  [tissue]  [distribution]  
Somatic Mutations in Cancer : COSMIC3DCDH23
Mutations and Diseases : HGMDCDH23
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
LOVD (Leiden Open Variation Database)**PUBLIC** CCHMC Molecular Genetics Laboratory Mutation Database
LOVD (Leiden Open Variation Database)MSeqDR-LSDB Mitochondrial Disease Locus Specific Database
BioMutasearch CDH23
DgiDB (Drug Gene Interaction Database)CDH23
DoCM (Curated mutations)CDH23 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)CDH23 (select a term)
intoGenCDH23
Cancer3DCDH23(select the gene name)
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM601067    601386    605516    617540   
Orphanet19167    12047   
DisGeNETCDH23
MedgenCDH23
Genetic Testing Registry CDH23
NextProtQ9H251 [Medical]
TSGene64072
GENETestsCDH23
Target ValidationCDH23
Huge Navigator CDH23 [HugePedia]
snp3D : Map Gene to Disease64072
BioCentury BCIQCDH23
ClinGenCDH23
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD64072
Chemical/Pharm GKB GenePA26296
Clinical trialCDH23
Miscellaneous
canSAR (ICR)CDH23 (select the gene name)
DataMed IndexCDH23
Probes
Litterature
PubMed78 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineCDH23
EVEXCDH23
GoPubMedCDH23
iHOPCDH23
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Wed Nov 13 17:36:30 CET 2019
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