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    CDH10 cadherin 10 [ Homo sapiens (human) ]

    Gene ID: 1008, updated on 2-Nov-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
    mouse all
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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_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (24487100..24644978, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (24591295..24750171, complement)
    RS_2024_09 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 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. 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
    2. 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
    3. 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
    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. 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

    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
    		  
    enables calcium ion binding IEA
    Inferred from Electronic Annotation
    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 synaptic membrane adhesion IBA
    Inferred from Biological aspect of Ancestor
    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_2024_08

    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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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