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CDH10 cadherin 10 [ Homo sapiens (human) ]

Gene ID: 1008, updated on 11-Apr-2024

Summary

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Official Symbol
CDH10provided by HGNC
Official Full Name
cadherin 10provided by HGNC
Primary source
HGNC:HGNC:1749
See related
Ensembl:ENSG00000040731 MIM:604555; AllianceGenome:HGNC:1749
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
Summary
This gene encodes a type II classical cadherin of the cadherin superfamily. Alternative splicing of this gene results in multiple transcript variants. At least one of these variants encodes a preproprotein that is proteolytically processed to generate the mature cadherin protein. These integral membrane proteins mediate calcium-dependent cell-cell adhesion and are composed of a large N-terminal extracellular domain, a single membrane-spanning domain, and a small, highly conserved C-terminal cytoplasmic domain. The extracellular domain consists of 5 subdomains, each containing a cadherin motif, and appears to determine the specificity of the protein's homophilic cell adhesion activity. Type II (atypical) cadherins are defined based on their lack of a histidine-alanine-valine (HAV) cell adhesion recognition sequence specific to type I cadherins. This particular cadherin is predominantly expressed in brain and is putatively involved in synaptic adhesions, axon outgrowth and guidance. Mutations in this gene may be associated with lung squamous cell carcinoma and colorectal cancer in human patients. [provided by RefSeq, Nov 2015]
Expression
Biased expression in brain (RPKM 13.5) and prostate (RPKM 2.1) See more
Orthologs
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Genomic context

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See CDH10 in Genome Data Viewer
Location:
5p14.2-p14.1
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (24487100..24644978, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (24591295..24750171, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (24487209..24645087, complement)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 2899 Neighboring gene AKT interacting protein pseudogene Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:24208573-24209476 Neighboring gene AKTIP pseudogene 2 Neighboring gene uncharacterized LOC105374689 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:24382088-24382767 Neighboring gene Sharpr-MPRA regulatory region 3372 Neighboring gene Neanderthal introgressed variant-containing enhancers experimental_84111 and experimental_84123 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:24644784-24645379 Neighboring gene uncharacterized LOC124901174 Neighboring gene TRPC6 pseudogene 6 Neighboring gene BTG anti-proliferation factor 4 pseudogene 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. Alterations of type II classical cadherin, cadherin-10 (CDH10), is associated with pancreatic ductal adenocarcinomas. Jinawath N, et al. Genes Chromosomes Cancer, 2017 May. PMID 28124395, Free PMC Article
  2. Whole Exome Sequencing Identifies Frequent Somatic Mutations in Cell-Cell Adhesion Genes in Chinese Patients with Lung Squamous Cell Carcinoma. Li C, et al. Sci Rep, 2015 Oct 27. PMID 26503331, Free PMC Article
  3. A genome-wide association study of autism reveals a common novel risk locus at 5p14.1. Ma D, et al. Ann Hum Genet, 2009 May. PMID 19456320, Free PMC Article
  4. Developmental patterns of cadherin expression and localization in relation to compartmentalized thalamocortical terminations in rat barrel cortex. Gil OD, et al. J Comp Neurol, 2002 Nov 25. PMID 12389209
  5. The human cadherin-10 gene: complete coding sequence, predominant expression in the brain, and mapping on chromosome 5p13-14. Kools P, et al. FEBS Lett, 1999 Jun 11. PMID 10386616

See all (27) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. G9a-mediated repression of CDH10 in hypoxia enhances breast tumour cell motility and associates with poor survival outcome.
    Title: G9a-mediated repression of CDH10 in hypoxia enhances breast tumour cell motility and associates with poor survival outcome.
  2. Loss of CDH10 gene is associated with pancreatic ductal adenocarcinomas.
    Title: Alterations of type II classical cadherin, cadherin-10 (CDH10), is associated with pancreatic ductal adenocarcinomas.
  3. Unconventional CDH10, CDH24 and DCHS2 genes harbored frameshift mutations.
    Title: Frameshift mutations of cadherin genes DCHS2, CDH10 and CDH24 genes in gastric and colorectal cancers with high microsatellite instability.
  4. The CC genotype of rs4307059 located in the region between CDH9 and CDH10 is associated with completed suicide in a Polish cohort
    Title: Analysis of four genes involved in the neurodevelopment shows association of rs4307059 polymorphism in the cadherin 9/10 region with completed suicide.
  5. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
  6. Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
    Title: Common genetic variants on 5p14.1 associate with autism spectrum disorders.
Submit: New GeneRIF Correction

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

EBI GWAS Catalog

Description
Common genetic variants on 5p14.1 associate with autism spectrum disorders.
EBI GWAS Catalog
Genetic determinants of plasma β₂-glycoprotein I levels: a genome-wide association study in extended pedigrees from Spain.
EBI GWAS Catalog
Genome-wide association study in obsessive-compulsive disorder: results from the OCGAS.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

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
  
Process Evidence Code Pubs
involved_in adherens junction organization IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in cell migration IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in cell morphogenesis IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in cell-cell adhesion NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in cell-cell adhesion mediated by cadherin IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in cell-cell junction assembly IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in homophilic cell adhesion via plasma membrane adhesion molecules IEA
Inferred from Electronic Annotation
more info
  
involved_in multicellular organism development IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in synaptic membrane adhesion IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in synaptic membrane adhesion IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in GABA-ergic synapse IEA
Inferred from Electronic Annotation
more info
  
is_active_in adherens junction IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of catenin complex IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in glutamatergic synapse IEA
Inferred from Electronic Annotation
more info
  
located_in plasma membrane TAS
Traceable Author Statement
more info
  
located_in postsynaptic specialization membrane IEA
Inferred from Electronic Annotation
more info
  
located_in presynaptic active zone membrane IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
cadherin-10
Names
T2-cadherin
cadherin 10 type 2

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)

  1. NM_001317222.2 → NP_001304151.1  cadherin-10 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and uses a downstream translation start site compared to variant 1. The encoded isoform (2) has a shorter N-terminus and lacks a predicted signal peptide compared to isoform 1.
    Source sequence(s)
    BC144168, BM669374, DA316487, DA531048
    Conserved Domains (1) summary
    pfam01049
    Location:41 → 188
    Cadherin_C; Cadherin cytoplasmic region

  2. NM_001317224.2 → NP_001304153.1  cadherin-10 isoform 3 preproprotein

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate in-frame splice site in the 3' coding region compared to variant 1. The encoded isoform (3, also known as CDH10_B) is shorter than isoform 1. This isoform (3) may undergo proteolytic processing similar to isoform 1.
    Source sequence(s)
    AC010387, AC091885
    UniProtKB/TrEMBL
    X5DNG6
    Conserved Domains (3) summary
    cd11304
    Location:164 → 265
    Cadherin_repeat; Cadherin tandem repeat domain
    smart00112
    Location:80 → 158
    CA; Cadherin repeats
    pfam01049
    Location:633 → 780
    Cadherin_C; Cadherin cytoplasmic region

  3. NM_001362460.1 → NP_001349389.1  cadherin-10 isoform 4 preproprotein

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks two in-frame exons in the 3' coding region compared to variant 1. The encoded isoform (4) is shorter than isoform 1. This isoform (4) may undergo proteolytic processing similar to isoform 1.
    Source sequence(s)
    AC010387, AC091885
    UniProtKB/TrEMBL
    D6RJG0
    Related
    ENSP00000425653.1, ENST00000510477.5
    Conserved Domains (2) summary
    cd11304
    Location:164 → 265
    Cadherin_repeat; Cadherin tandem repeat domain
    smart00112
    Location:80 → 158
    CA; Cadherin repeats

  4. NM_006727.5 → NP_006718.2  cadherin-10 isoform 1 preproprotein

    See identical proteins and their annotated locations for NP_006718.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AB035303, BM669374, DA316487, DA531048
    Consensus CDS
    CCDS3892.1
    UniProtKB/Swiss-Prot
    Q9ULB3, Q9Y6N8
    UniProtKB/TrEMBL
    X5D8X5
    Related
    ENSP00000264463.4, ENST00000264463.8
    Conserved Domains (3) summary
    cd11304
    Location:164 → 265
    Cadherin_repeat; Cadherin tandem repeat domain
    smart00112
    Location:80 → 158
    CA; Cadherin repeats
    pfam01049
    Location:635 → 782
    Cadherin_C; Cadherin cytoplasmic region

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    24487100..24644978 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011513923.3 → XP_011512225.1  cadherin-10 isoform X1

    See identical proteins and their annotated locations for XP_011512225.1

    UniProtKB/Swiss-Prot
    Q9ULB3, Q9Y6N8
    UniProtKB/TrEMBL
    X5D8X5
    Conserved Domains (3) summary
    cd11304
    Location:164 → 265
    Cadherin_repeat; Cadherin tandem repeat domain
    smart00112
    Location:80 → 158
    CA; Cadherin repeats
    pfam01049
    Location:635 → 782
    Cadherin_C; Cadherin cytoplasmic region

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    24591295..24750171 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054351383.1 → XP_054207358.1  cadherin-10 isoform X1

    UniProtKB/Swiss-Prot
    Q9ULB3, Q9Y6N8
    UniProtKB/TrEMBL
    X5D8X5

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001190450.1: Suppressed sequence

    Description
    NM_001190450.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9Y6N8.2 GenPept UniProtKB/Swiss-Prot:Q9Y6N8

Gene LinkOut

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