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CDH23 cadherin related 23 [ Homo sapiens (human) ]

Gene ID: 64072, updated on 5-Aug-2018

Summary

Official Symbol
CDH23provided by HGNC
Official Full Name
cadherin related 23provided by HGNC
Primary source
HGNC:HGNC:13733
See related
Ensembl:ENSG00000107736 MIM:605516; Vega:OTTHUMG00000019347
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
PITA5; USH1D; CDHR23
Summary
This gene is a member of the cadherin superfamily, whose genes encode calcium dependent cell-cell adhesion glycoproteins. The encoded protein is thought to be involved in stereocilia organization and hair bundle formation. The gene is located in a region containing the human deafness loci DFNB12 and USH1D. Usher syndrome 1D and nonsyndromic autosomal recessive deafness DFNB12 are caused by allelic mutations of this cadherin-like gene. Upregulation of this gene may also be associated with breast cancer. Alternative splice variants encoding different isoforms have been described. [provided by RefSeq, May 2013]
Expression
Broad expression in ovary (RPKM 4.2), fat (RPKM 2.9) and 18 other tissues See more
Orthologs

Genomic context

See CDH23 in Genome Data Viewer
Location:
10q22.1
Exon count:
71
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 10 NC_000010.11 (71396934..71815947)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (73156691..73575704)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC112268061 Neighboring gene unc-5 netrin receptor B Neighboring gene uncharacterized LOC105378353 Neighboring gene solute carrier family 29 member 3 Neighboring gene uncharacterized LOC105378356 Neighboring gene CDH23 antisense RNA 1 Neighboring gene uncharacterized LOC105378355 Neighboring gene chromosome 10 open reading frame 105 Neighboring gene Sharpr-MPRA regulatory region 2121 Neighboring gene V-set immunoregulatory receptor Neighboring gene microRNA 7152 Neighboring gene NFE2L2 motif-containing MPRA enhancers 43 and 138 Neighboring gene RNA, U7 small nuclear 38 pseudogene Neighboring gene prosaposin

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Deafness, autosomal recessive 12 Compare labs
PITUITARY ADENOMA 5, MULTIPLE TYPES
MedGen: C4539685 OMIM: 617540 GeneReviews: Not available
not available
Usher syndrome, type 1D
MedGen: C1832845 OMIM: 601067 GeneReviews: Usher Syndrome Type I
Compare labs

NHGRI GWAS Catalog

Description
Association analyses identify three susceptibility Loci for vitiligo in the Chinese Han population.
NHGRI GWA Catalog
Genome-wide association study of bipolar disorder accounting for effect of body mass index identifies a new risk allele in TCF7L2.
NHGRI GWA Catalog
Genome-wide association study of lung function decline in adults with and without asthma.
NHGRI GWA Catalog
Genome-wide association study of smoking behaviours in patients with COPD.
NHGRI GWA Catalog

HIV-1 interactions

Replication interactions

Interaction Pubs
Knockdown of cadherin-related 23 (CDH23) by siRNA enhances HIV-1 replication in CD4+/CCR5+/CXCR4+ TZM-bl HeLa cells PubMed

Go to the HIV-1, Human Interaction Database

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ00233, FLJ36499, KIAA1774, KIAA1812, MGC102761, DKFZp434P2350

Gene Ontology Provided by GOA

Function Evidence Code Pubs
calcium ion binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
calcium ion transport IMP
Inferred from Mutant Phenotype
more info
PubMed 
calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules NAS
Non-traceable Author Statement
more info
PubMed 
equilibrioception IMP
Inferred from Mutant Phenotype
more info
PubMed 
homophilic cell adhesion via plasma membrane adhesion molecules IEA
Inferred from Electronic Annotation
more info
 
inner ear receptor cell stereocilium organization IEA
Inferred from Electronic Annotation
more info
 
locomotory behavior IEA
Inferred from Electronic Annotation
more info
 
photoreceptor cell maintenance IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of cytosolic calcium ion concentration IMP
Inferred from Mutant Phenotype
more info
PubMed 
response to stimulus IEA
Inferred from Electronic Annotation
more info
 
sensory perception of light stimulus IMP
Inferred from Mutant Phenotype
more info
PubMed 
sensory perception of sound IMP
Inferred from Mutant Phenotype
more info
PubMed 
visual perception IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
integral component of membrane IEA
Inferred from Electronic Annotation
more info
 
membrane NAS
Non-traceable Author Statement
more info
PubMed 
plasma membrane IEA
Inferred from Electronic Annotation
more info
 
stereocilium ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 

General protein information

Preferred Names
cadherin-23
Names
cadherin-like 23
cadherin-related family member 23
otocadherin

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_008835.1 RefSeqGene

    Range
    4988..424001
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001171930.1NP_001165401.1  cadherin-23 isoform 3 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 3' coding region and 3' UTR, compared to variant 1. The resulting isoform (3) has a distinct C-terminus and is shorter than isoform 1.
    Source sequence(s)
    AF312024, AL731541, BC011570, BC065284, BC136976, DB333699
    Consensus CDS
    CCDS81472.1
    UniProtKB/Swiss-Prot
    Q9H251
    UniProtKB/TrEMBL
    A0A087WYR8, Q6P152
    Related
    ENSP00000482036.2, OTTHUMP00000275676, ENST00000616684.4, OTTHUMT00000476497
    Conserved Domains (1) summary
    cd11304
    Location:894990
    Cadherin_repeat; Cadherin tandem repeat domain
  2. NM_001171931.1NP_001165402.1  cadherin-23 isoform 4 precursor

    See identical proteins and their annotated locations for NP_001165402.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 3' coding region and 3' UTR, compared to variant 1. The resulting isoform (4) has a distinct C-terminus and is shorter than isoform 1.
    Source sequence(s)
    AL359183, AL731541, BC011570, BC032581
    Consensus CDS
    CCDS81473.1
    UniProtKB/Swiss-Prot
    Q9H251
    UniProtKB/TrEMBL
    Q8N5B3
    Related
    ENSP00000299366.8, OTTHUMP00000272192, ENST00000299366.11, OTTHUMT00000051229
    Conserved Domains (1) summary
    cd11304
    Location:894990
    Cadherin_repeat; Cadherin tandem repeat domain
  3. NM_001171932.1NP_001165403.1  cadherin-23 isoform 5 precursor

    See identical proteins and their annotated locations for NP_001165403.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) differs in the 3' coding region and 3' UTR, compared to variant 1. The resulting isoform (5) has a distinct C-terminus and is shorter than isoform 1.
    Source sequence(s)
    AL772287, BC011570, BC139903
    UniProtKB/Swiss-Prot
    Q9H251
    UniProtKB/TrEMBL
    A5D6V9
    Conserved Domains (1) summary
    cd11304
    Location:136231
    Cadherin_repeat; Cadherin tandem repeat domain
  4. NM_001171933.1NP_001165404.1  cadherin-23 isoform 6

    See identical proteins and their annotated locations for NP_001165404.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (6, also referred to as isoform B1) is shorter than isoform 1.
    Source sequence(s)
    AL731541, AY563161, AY563165, BM673126
    Consensus CDS
    CCDS53540.1
    UniProtKB/Swiss-Prot
    Q9H251
    Related
    ENSP00000381768.3, ENST00000398788.4
    Conserved Domains (1) summary
    cd11304
    Location:166264
    Cadherin_repeat; Cadherin tandem repeat domain
  5. NM_001171934.1NP_001165405.1  cadherin-23 isoform 7

    See identical proteins and their annotated locations for NP_001165405.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon, compared to variant 1. This variant also lacks an in-frame exon in the 3' coding region compared to variant 1. The encoded isoform (7, also referred to as isoform B2) is shorter than isoform 1.
    Source sequence(s)
    AL731541, AY563161, AY563165, BM673126
    Consensus CDS
    CCDS73146.1
    UniProtKB/Swiss-Prot
    Q9H251
    Related
    ENSP00000478374.1, ENST00000619887.4
    Conserved Domains (1) summary
    cd11304
    Location:166264
    Cadherin_repeat; Cadherin tandem repeat domain
  6. NM_001171935.1NP_001165406.1  cadherin-23 isoform 8

    See identical proteins and their annotated locations for NP_001165406.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (8) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (8, also referred to as isoform C1) has a distinct N-terminus and is shorter than isoform 1.
    Source sequence(s)
    AY563161, BM673126
    UniProtKB/Swiss-Prot
    Q9H251
  7. NM_001171936.1NP_001165407.1  cadherin-23 isoform 9

    See identical proteins and their annotated locations for NP_001165407.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (9) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. This variant also lacks an in-frame exon in the 3' coding region compared to variant 1. The encoded isoform (9, also referred to as isoform C2) has a distinct N-terminus and is shorter than isoform 1.
    Source sequence(s)
    AY563162, BM673126
    UniProtKB/Swiss-Prot
    Q9H251
  8. NM_022124.5NP_071407.4  cadherin-23 isoform 1 precursor

    See identical proteins and their annotated locations for NP_071407.4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AF312024, AL731541, AY563161, BC011570, BC065284, BC136976, BM673126
    Consensus CDS
    CCDS86100.1
    UniProtKB/Swiss-Prot
    Q9H251
    UniProtKB/TrEMBL
    Q6P152
    Related
    ENSP00000224721.9, OTTHUMP00000020837, ENST00000224721.11, OTTHUMT00000051227
    Conserved Domains (1) summary
    cd11304
    Location:14261523
    Cadherin_repeat; Cadherin tandem repeat domain
  9. NM_052836.3NP_443068.1  cadherin-23 isoform 2 precursor

    See identical proteins and their annotated locations for NP_443068.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 3' coding region and 3' UTR, compared to variant 1. The resulting isoform (2) has a distinct C-terminus and is shorter than isoform 1.
    Source sequence(s)
    AL772287, AY358617, BC011570, BC136976
    Consensus CDS
    CCDS44429.1
    UniProtKB/Swiss-Prot
    Q9H251
    Related
    ENSP00000473454.2, OTTHUMP00000272191, ENST00000461841.7, OTTHUMT00000051228
    Conserved Domains (1) summary
    cd11304
    Location:136231
    Cadherin_repeat; Cadherin tandem repeat domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000010.11 Reference GRCh38.p12 Primary Assembly

    Range
    71396934..71815947
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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