Cdh23 cadherin related 23 (otocadherin) [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Cdh23provided by MGI
Official Full Name: cadherin related 23 (otocadherin)provided by MGI
Primary source: MGI:MGI:1890219
See related: Ensembl:ENSMUSG00000012819 AllianceGenome:MGI:1890219
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: v; ahl; bob; bus; ahl1; mdfw; sals; USH1D; nmf112; nmf181; nmf252; 4930542A03Rik
Summary: Predicted to enable cadherin binding activity; calcium ion binding activity; and protein N-terminus binding activity. Acts upstream of or within several processes, including animal organ morphogenesis; righting reflex; and sensory perception of sound. Located in several cellular components, including cochlear hair cell ribbon synapse; kinocilium; and stereocilium tip. Is active in photoreceptor ribbon synapse. Is expressed in several structures, including brain; genitourinary system; lung; sensory organ; and thymus. Used to study Usher syndrome type 1D and autosomal recessive nonsyndromic deafness 12. Human ortholog(s) of this gene implicated in Usher syndrome type 1D; autosomal recessive nonsyndromic deafness; autosomal recessive nonsyndromic deafness 12; and pituitary adenoma 5. Orthologous to human CDH23 (cadherin related 23). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in testis adult (RPKM 8.3), heart adult (RPKM 1.0) and 8 other tissues See more
Orthologs: human all
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Genomic context

Location:: 10 B4; 10 30.11 cM

Exon count:: 73

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	10	NC_000076.7 (60138527..60532291, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	10	NC_000076.6 (60302748..60696513, complement)

Chromosome 10 - NC_000076.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Disruption of Cdh23 exon 68 splicing leads to progressive hearing loss in mice by affecting tip-link stability.
Title: Disruption of Cdh23 exon 68 splicing leads to progressive hearing loss in mice by affecting tip-link stability.
Impacts of an age-related hearing loss allele of cadherin 23 on severity of hearing loss in ICR and NOD/Shi mice.
Title: Impacts of an age-related hearing loss allele of cadherin 23 on severity of hearing loss in ICR and NOD/Shi mice.
Variants in CDH23 cause a broad spectrum of hearing loss: from non-syndromic to syndromic hearing loss as well as from congenital to age-related hearing loss.
Title: Variants in CDH23 cause a broad spectrum of hearing loss: from non-syndromic to syndromic hearing loss as well as from congenital to age-related hearing loss.
Neuroplastin genetically interacts with Cadherin 23 and the encoded isoform Np55 is sufficient for cochlear hair cell function and hearing.
Title: Neuroplastin genetically interacts with Cadherin 23 and the encoded isoform Np55 is sufficient for cochlear hair cell function and hearing.
Phenotypic differences in the inner ears of CBA/CaJ and C57BL/6J mice carrying missense and single base pair deletion mutations in the Cdh23 gene.
Title: Phenotypic differences in the inner ears of CBA/CaJ and C57BL/6J mice carrying missense and single base pair deletion mutations in the Cdh23 gene.
Endonuclease V Regulates Atherosclerosis Through C-C Motif Chemokine Ligand 2-Mediated Monocyte Infiltration.
Title: Endonuclease V Regulates Atherosclerosis Through C-C Motif Chemokine Ligand 2-Mediated Monocyte Infiltration.
c.753A>G genome editing of a Cdh23(ahl) allele delays age-related hearing loss and degeneration of cochlear hair cells in C57BL/6J mice.
Title: c.753A>G genome editing of a Cdh23(ahl) allele delays age-related hearing loss and degeneration of cochlear hair cells in C57BL/6J mice.
Alternative Splicing of Cdh23 Exon 68 Is Regulated by RBM24, RBM38, and PTBP1.
Title: Alternative Splicing of Cdh23 Exon 68 Is Regulated by RBM24, RBM38, and PTBP1.
suggest that mice heterozygous for the Cdh23 mutation do not have truly normal hearing
Title: Mice heterozygous for the Cdh23/Ahl1 mutation show age-related deficits in auditory temporal processing.
Crystal structures showing 18 CDH23 extracellular cadherin (EC) repeats, including the most and least conserved, a fragment carrying disease mutations, and EC repeats with non-canonical Ca(2+)-binding motif sequences and unusual secondary structure. Deafness mutations' effects on stability and affinity for Ca(2+). Additionally, contiguous CDH23 EC repeats reveals helicity and potential parallel dimerization faces.
Title: Zooming in on Cadherin-23: Structural Diversity and Potential Mechanisms of Inherited Deafness.

Submit: New GeneRIF Correction See all GeneRIFs (51)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Spontaneous (13) 1 citation
Chemically induced (other) (1) 1 citation
Targeted (8) 1 citation
QTL (1) 1 citation
Chemically induced (ENU) (8) 1 citation
Not Applicable (1) 1 citation
Endonuclease-mediated (9) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

AI037048 (e-PCR)
- UniSTS:180044

U27340 (e-PCR)
- UniSTS:208524

Psap (e-PCR), detects polymorphism
- UniSTS:144271

Cdh23 (e-PCR), detects polymorphism
- UniSTS:256658

Cdh23 (e-PCR), detects polymorphism
- UniSTS:256659

Cdh23 (e-PCR), detects polymorphism
- UniSTS:256660

Cdh23 (e-PCR), detects polymorphism
- UniSTS:256661

RH136606 (e-PCR)
- UniSTS:210586

RH126059 (e-PCR)
- UniSTS:162771

NoName (e-PCR)
- UniSTS:224753

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables beta-catenin binding	IBA Inferred from Biological aspect of Ancestor more info
enables cadherin binding	IBA Inferred from Biological aspect of Ancestor more info
enables calcium ion binding	IEA Inferred from Electronic Annotation more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
acts_upstream_of_or_within adult locomotory behavior	IMP Inferred from Mutant Phenotype more info
acts_upstream_of_or_within auditory receptor cell stereocilium organization	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within auditory receptor cell stereocilium organization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in calcium ion transport	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules	ISS Inferred from Sequence or Structural Similarity more info	PubMed
acts_upstream_of_or_within cell adhesion	TAS Traceable Author Statement more info	PubMed
involved_in cell migration	IBA Inferred from Biological aspect of Ancestor more info
involved_in cell-cell adhesion via plasma-membrane adhesion molecules	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within cochlea development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in equilibrioception	ISO Inferred from Sequence Orthology more info
involved_in homophilic cell adhesion via plasma membrane adhesion molecules	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within inner ear auditory receptor cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within inner ear development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within inner ear morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within inner ear receptor cell stereocilium organization	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within locomotory behavior	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in multicellular organism development	IBA Inferred from Biological aspect of Ancestor more info
involved_in neuron projection development	IBA Inferred from Biological aspect of Ancestor more info
involved_in photoreceptor cell maintenance	ISO Inferred from Sequence Orthology more info
involved_in regulation of cytosolic calcium ion concentration	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within righting reflex	IMP Inferred from Mutant Phenotype more info
acts_upstream_of_or_within sensory perception of light stimulus	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in sensory perception of light stimulus	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within sensory perception of sound	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within sensory perception of sound	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within sensory perception of sound	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in apical part of cell	ISO Inferred from Sequence Orthology more info
part_of catenin complex	IBA Inferred from Biological aspect of Ancestor more info
located_in centrosome	IDA Inferred from Direct Assay more info	PubMed
located_in cochlear hair cell ribbon synapse	IC Inferred by Curator more info	PubMed
is_active_in cochlear hair cell ribbon synapse	IDA Inferred from Direct Assay more info	PubMed
located_in kinocilium	IDA Inferred from Direct Assay more info	PubMed
located_in membrane	IEA Inferred from Electronic Annotation more info
located_in photoreceptor inner segment	IDA Inferred from Direct Assay more info	PubMed
is_active_in photoreceptor ribbon synapse	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	TAS Traceable Author Statement more info
located_in stereocilium	IDA Inferred from Direct Assay more info	PubMed
located_in stereocilium tip	IDA Inferred from Direct Assay more info	PubMed
is_active_in synapse	IDA Inferred from Direct Assay more info	PubMed
located_in synapse	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: cadherin-23

Names: age related hearing loss 1; bobby; bustling; cadherin 23 (otocadherin); modifier of deaf waddler; otocadherin; waltzer

NCBI Reference Sequences (RefSeq)

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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.

mRNA and Protein(s)

NM_001252635.1 → NP_001239564.1 cadherin-23 isoform 2 precursor

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks an in-frame exon in the coding region, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.

Source sequence(s)

AC079082, AC079818, AC079819, AEKQ02027206, AK016365

Consensus CDS

CCDS56704.1

UniProtKB/TrEMBL

K4DI74, Q5DUA3

Related

ENSMUSP00000101104.3, ENSMUST00000105464.9

Conserved Domains (1) summary

cd11304
Location:1531 → 1628

Cadherin_repeat; Cadherin tandem repeat domain
NM_023370.3 → NP_075859.2 cadherin-23 isoform 1 precursor

See identical proteins and their annotated locations for NP_075859.2

Status: VALIDATED

Description

Transcript Variant: This variant (1) encodes the longer isoform (1).

Source sequence(s)

AEKQ02027206, AF308939, AK016365

UniProtKB/Swiss-Prot

E9QP63, Q5QGS3, Q5QGS4, Q5QGS7, Q5QGS8, Q99NH1, Q99PF4, Q9D4N9

Conserved Domains (1) summary

cd11304
Location:1533 → 1630

Cadherin_repeat; Cadherin tandem repeat domain

RNA

NR_045556.1 RNA Sequence

Status: VALIDATED

Description

Transcript Variant: This variant (3) uses an alternate splice site in the 3' coding region, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AC079082, AC079818, AC079819, AEKQ02027206, AK016365

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000076.7 Reference GRCm39 C57BL/6J

Range

60138527..60532291 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017313930.2 → XP_017169419.1 cadherin-23 isoform X4

UniProtKB/TrEMBL

Q5DUA3

Related

ENSMUSP00000072973.5, ENSMUST00000073242.11

Conserved Domains (1) summary

cd11304
Location:1540 → 1637

Cadherin_repeat; Cadherin tandem repeat domain
XM_030245069.1 → XP_030100929.1 cadherin-23 isoform X1

UniProtKB/TrEMBL

E9Q7M6

Related

ENSMUSP00000101102.2, ENSMUST00000105462.8

Conserved Domains (1) summary

cd11304
Location:1533 → 1630

Cadherin_repeat; Cadherin tandem repeat domain
XM_017313927.2 → XP_017169416.1 cadherin-23 isoform X1

UniProtKB/TrEMBL

E9Q7M6

Conserved Domains (1) summary

cd11304
Location:1533 → 1630

Cadherin_repeat; Cadherin tandem repeat domain
XM_017313929.1 → XP_017169418.1 cadherin-23 isoform X3

UniProtKB/Swiss-Prot

Q99PF4

Conserved Domains (1) summary

cd11304
Location:166 → 264

Cadherin_repeat; Cadherin tandem repeat domain
XM_006513602.2 → XP_006513665.1 cadherin-23 isoform X3

See identical proteins and their annotated locations for XP_006513665.1

UniProtKB/Swiss-Prot

Q99PF4

Related

ENSMUST00000153525.8

Conserved Domains (1) summary

cd11304
Location:166 → 264

Cadherin_repeat; Cadherin tandem repeat domain
XM_017313931.3 → XP_017169420.1 cadherin-23 isoform X5
XM_017313928.3 → XP_017169417.1 cadherin-23 isoform X2

UniProtKB/TrEMBL

Q5DUA5

Related

ENSMUST00000135638.8

Conserved Domains (1) summary

cd11304
Location:1531 → 1628

Cadherin_repeat; Cadherin tandem repeat domain