CDH23 cadherin related 23 [Homo sapiens (human)] - Gene

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; AllianceGenome:HGNC:13733
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: mouse all
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Genomic context

Location:: 10q22.1

Exon count:: 71

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	10	NC_000010.11 (71396920..71815947)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	10	NC_060934.1 (72266464..72686680)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	10	NC_000010.10 (73156677..73575704)

Chromosome 10 - NC_000010.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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 Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Identification of Coding Variants in 10q22.1 Associated with Vitiligo in the Chinese Han Population.
Title: Identification of Coding Variants in 10q22.1 Associated with Vitiligo in the Chinese Han Population.
A Novel Biallelic Variant in CDH23 Gene in a Family with Atypical USH1D Manifestation: A Literature Review and Investigation of Genotype-Phenotype Correlation.
Title: A Novel Biallelic Variant in CDH23 Gene in a Family with Atypical USH1D Manifestation: A Literature Review and Investigation of Genotype-Phenotype Correlation.
Cochlear Implantation Outcomes in Children With CDH23 Mutations-Associated Hearing Loss.
Title: Cochlear Implantation Outcomes in Children With CDH23 Mutations-Associated Hearing Loss.
Association between genetic polymorphisms of cadherin 23 and noise-induced hearing loss: a meta-analysis.
Title: Association between genetic polymorphisms of cadherin 23 and noise-induced hearing loss: a meta-analysis.
Methylation silencing CDH23 is a poor prognostic marker in diffuse large B-cell lymphoma.
Title: Methylation silencing CDH23 is a poor prognostic marker in diffuse large B-cell lymphoma.
A novel missense mutation locus of cadherin 23 and the interaction of cadherin 23 and protocadherin 15 in a patient with usher syndrome.
Title: A novel missense mutation locus of cadherin 23 and the interaction of cadherin 23 and protocadherin 15 in a patient with usher syndrome.
Novel homozygous variants in the TMC1 and CDH23 genes cause autosomal recessive nonsyndromic hearing loss.
Title: Novel homozygous variants in the TMC1 and CDH23 genes cause autosomal recessive nonsyndromic hearing loss.
[Nonsyndromic deafness due to compound heterozygous mutation of the CDH23 gene].
Title: [Nonsyndromic deafness due to compound heterozygous mutation of the CDH23 gene].
High-Throughput Sequencing Identifies 3 Novel Susceptibility Genes for Hereditary Melanoma.
Title: High-Throughput Sequencing Identifies 3 Novel Susceptibility Genes for Hereditary Melanoma.
A novel highly frequent singlenucleotide polymorphism site of cadherin 23 in clear cell renal cell carcinoma with sarcomatoid differentiation based on whole exome sequencing.
Title: A novel highly frequent single‑nucleotide polymorphism site of cadherin 23 in clear cell renal cell carcinoma with sarcomatoid differentiation based on whole exome sequencing.

Submit: New GeneRIF Correction See all GeneRIFs (56)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Autosomal recessive nonsyndromic hearing loss 12 MedGen: C1832394 OMIM: 601386 GeneReviews: Genetic Hearing Loss Overview	Compare labs
Pituitary adenoma 5, multiple types MedGen: C4539685 OMIM: 617540 GeneReviews: Not available	Compare labs
Usher syndrome type 1D MedGen: C1832845 OMIM: 601067 GeneReviews: Usher Syndrome Type I	Compare labs

EBI GWAS Catalog

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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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

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D10S412 (e-PCR)
- UniSTS:148257

D10S412 (e-PCR)
- UniSTS:148258

D8S2279 (e-PCR)
- UniSTS:473907

SGC38181 (e-PCR)
- UniSTS:35130

RH45898 (e-PCR)
- UniSTS:35131

D10S584 (e-PCR), detects polymorphism
- UniSTS:64315

SHGC-152305 (e-PCR)
- UniSTS:177468

SHGC-80642 (e-PCR)
- UniSTS:102206

STS-R80211 (e-PCR)
- UniSTS:42822

D1S1423 (e-PCR)
- UniSTS:149619

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

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

SHGC-152620 (e-PCR)
- UniSTS:177560

RH48031 (e-PCR)
- UniSTS:73628

D10S1694 (e-PCR), detects polymorphism
- UniSTS:33695

STS-W72919 (e-PCR)
- UniSTS:31653

D10S2338 (e-PCR)
- UniSTS:56487

SHGC-151188 (e-PCR)
- UniSTS:173494

G62740 (e-PCR)
- UniSTS:139717

SHGC-151195 (e-PCR)
- UniSTS:173511

SHGC-81728 (e-PCR)
- UniSTS:103902

CDH23 (e-PCR)
- UniSTS:503013

D10S584 (e-PCR), detects polymorphism
- UniSTS:20714

STS-N39237 (e-PCR)
- UniSTS:39406

GDB:313461 (e-PCR)
- UniSTS:54001

D10S1650 (e-PCR), detects polymorphism
- UniSTS:42228

RH44693 (e-PCR)
- UniSTS:42999

D10S338 (e-PCR)
- UniSTS:147960

SHGC-154025 (e-PCR)
- UniSTS:182266

Clone Names

FLJ00233, FLJ36499, KIAA1774, KIAA1812, MGC102761, DKFZp434P2350

Gene Ontology Provided by GOA

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 protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in auditory receptor cell stereocilium organization	IEA Inferred from Electronic Annotation more info
involved_in calcium ion transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules	NAS Non-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
involved_in cochlea development	IEA Inferred from Electronic Annotation more info
involved_in equilibrioception	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in homophilic cell adhesion via plasma membrane adhesion molecules	IEA Inferred from Electronic Annotation more info
involved_in locomotory behavior	IEA Inferred from Electronic Annotation more info
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	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of cytosolic calcium ion concentration	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in response to stimulus	IEA Inferred from Electronic Annotation more info
involved_in sensory perception of light stimulus	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within sensory perception of sound	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in sensory perception of sound	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in visual perception	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
part_of catenin complex	IBA Inferred from Biological aspect of Ancestor more info
located_in centrosome	IEA Inferred from Electronic Annotation more info
located_in cochlear hair cell ribbon synapse	IEA Inferred from Electronic Annotation more info
located_in kinocilium	IEA Inferred from Electronic Annotation more info
located_in membrane	NAS Non-traceable Author Statement more info	PubMed
located_in photoreceptor inner segment	IEA Inferred from Electronic Annotation more info
located_in photoreceptor ribbon synapse	IEA Inferred from Electronic Annotation more info
located_in stereocilium	ISS Inferred from Sequence or Structural Similarity more info	PubMed
located_in stereocilium tip	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: cadherin-23

Names: cadherin-like 23; cadherin-related family member 23; otocadherin

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.

Genomic

NG_008835.1 RefSeqGene

Range

4974..424001

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001171930.2 → NP_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, AL359183, AL731541, BC011570, BC065284, BC136976, DB333699

Consensus CDS

CCDS81472.1

UniProtKB/TrEMBL

A0A087WYR8, A0A0A0MS94, Q6P152

Related

ENSP00000482036.2, ENST00000616684.4

Conserved Domains (1) summary

cd11304
Location:894 → 990

Cadherin_repeat; Cadherin tandem repeat domain
NM_001171931.2 → NP_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/TrEMBL

B1AVV0, G3XCN8, Q8N5B3

Related

ENSP00000299366.8, ENST00000299366.11

Conserved Domains (1) summary

cd11304
Location:894 → 990

Cadherin_repeat; Cadherin tandem repeat domain
NM_001171932.2 → NP_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)

AL359183, AL772287, BC011570, BC139903

UniProtKB/TrEMBL

A5D6V9

Conserved Domains (1) summary

cd11304
Location:136 → 231

Cadherin_repeat; Cadherin tandem repeat domain
NM_001171933.1 → NP_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:166 → 264

Cadherin_repeat; Cadherin tandem repeat domain
NM_001171934.1 → NP_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:166 → 264

Cadherin_repeat; Cadherin tandem repeat domain
NM_001171935.1 → NP_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
NM_001171936.1 → NP_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
NM_022124.6 → NP_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, AL359183, AL731541, AY563161, BC011570, BC065284, BC136976, BM673126

Consensus CDS

CCDS86100.1

UniProtKB/Swiss-Prot

C4IXS9, F6U049, Q5QGS1, Q5QGS2, Q5QGS5, Q5QGS6, Q5XKN2, Q6UWW1, Q96JL3, Q9H251, Q9H4K9

Related

ENSP00000224721.9, ENST00000224721.12

Conserved Domains (1) summary

cd11304
Location:1426 → 1523

Cadherin_repeat; Cadherin tandem repeat domain
NM_052836.4 → NP_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)

AL359183, AL772287, AY358617, BC011570, BC136976

Consensus CDS

CCDS44429.1

UniProtKB/TrEMBL

Q32P55

Related

ENSP00000473454.2, ENST00000461841.7

Conserved Domains (1) summary

cd11304
Location:136 → 231

Cadherin_repeat; Cadherin tandem repeat domain