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CDH20 cadherin 20 [ Homo sapiens (human) ]

Gene ID: 28316, updated on 11-Apr-2024

Summary

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Official Symbol
CDH20provided by HGNC
Official Full Name
cadherin 20provided by HGNC
Primary source
HGNC:HGNC:1760
See related
Ensembl:ENSG00000101542 MIM:605807; AllianceGenome:HGNC:1760
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
Cdh7; CDH7L3
Summary
This gene is a type II classical cadherin from the cadherin superfamily and one of three cadherin 7-like genes located in a cluster on chromosome 18. The encoded membrane protein is a calcium dependent cell-cell adhesion glycoprotein comprised of five extracellular cadherin repeats, a transmembrane region and a highly conserved cytoplasmic tail. Type II (atypical) cadherins are defined based on their lack of a HAV cell adhesion recognition sequence specific to type I cadherins. Since disturbance of intracellular adhesion is a prerequisite for invasion and metastasis of tumor cells, cadherins are considered prime candidates for tumor suppressor genes. [provided by RefSeq, Jul 2008]
Expression
Biased expression in brain (RPKM 10.7) and fat (RPKM 4.1) See more
Orthologs
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Genomic context

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Location:
18q21.33
Exon count:
15
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (61333430..61555779)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (61536681..61759001)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (59000663..59223012)

Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene ADP ribosylation factor like GTPase 14 effector protein pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:58352137-58352638 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:58352639-58353138 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr18:58471303-58472038 Neighboring gene high mobility group nucleosome binding domain 1 pseudogene 31 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr18:58647560-58648273 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:58931179-58931678 Neighboring gene NANOG hESC enhancer GRCh37_chr18:58936564-58937065 Neighboring gene RNA, U6 small nuclear 116, pseudogene Neighboring gene ribosomal protein L30 pseudogene 14 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:59221319-59221826 Neighboring gene uncharacterized LOC124904314 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr18:59273512-59274711 Neighboring gene LSM6 homolog, U6 small nuclear RNA and mRNA degradation associated 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. Characterization of three novel human cadherin genes (CDH7, CDH19, and CDH20) clustered on chromosome 18q22-q23 and with high homology to chicken cadherin-7. Kools P, et al. Genomics, 2000 Sep 15. PMID 10995570
  2. Genetic analysis of diabetic nephropathy on chromosome 18 in African Americans: linkage analysis and dense SNP mapping. McDonough CW, et al. Hum Genet, 2009 Dec. PMID 19690890, Free PMC Article
  3. E3 ubiquitin ligase RNF123 targets lamin B1 and lamin-binding proteins. Khanna R, et al. FEBS J, 2018 Jun. PMID 29676528
  4. Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. Comuzzie AG, et al. PLoS One, 2012. PMID 23251661, Free PMC Article
  5. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. Rose JE, et al. Mol Med, 2010 Jul-Aug. PMID 20379614, Free PMC Article

See all (10) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. Observational study of gene-disease association. (HuGE Navigator)
    Title: Genetic analysis of diabetic nephropathy on chromosome 18 in African Americans: linkage analysis and dense SNP mapping.
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
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
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

Clone Names

  • FLJ37047

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 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
  
Component Evidence Code Pubs
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
  

General protein information

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Preferred Names
cadherin-20
Names
cadherin 20, 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_031891.4 → NP_114097.2  cadherin-20 preproprotein

    See identical proteins and their annotated locations for NP_114097.2

    Status: REVIEWED

    Source sequence(s)
    AC006203, AC025656, AC090409
    Consensus CDS
    CCDS11977.1
    UniProtKB/Swiss-Prot
    Q495S3, Q9HBT6
    UniProtKB/TrEMBL
    A8K2C5
    Related
    ENSP00000262717.3, ENST00000262717.9
    Conserved Domains (3) summary
    cd11304
    Location:394 → 490
    Cadherin_repeat; Cadherin tandem repeat domain
    smart00112
    Location:85 → 163
    CA; Cadherin repeats
    pfam01049
    Location:643 → 794
    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_000018.10 Reference GRCh38.p14 Primary Assembly

    Range
    61333430..61555779
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024451165.2 → XP_024306933.1  cadherin-20 isoform X1

    UniProtKB/Swiss-Prot
    Q495S3, Q9HBT6
    UniProtKB/TrEMBL
    A8K2C5
    Related
    ENSP00000444767.1, ENST00000536675.2
    Conserved Domains (3) summary
    cd11304
    Location:394 → 490
    Cadherin_repeat; Cadherin tandem repeat domain
    smart00112
    Location:85 → 163
    CA; Cadherin repeats
    pfam01049
    Location:643 → 794
    Cadherin_C; Cadherin cytoplasmic region

RNA

  1. XR_001753187.2 RNA Sequence

  2. XR_001753186.2 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060942.1 Alternate T2T-CHM13v2.0

    Range
    61536681..61759001
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054318533.1 → XP_054174508.1  cadherin-20 isoform X1

    UniProtKB/Swiss-Prot
    Q495S3, Q9HBT6

RNA

  1. XR_008484998.1 RNA Sequence

  2. XR_008484997.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9HBT6.2 GenPept UniProtKB/Swiss-Prot:Q9HBT6

Gene LinkOut

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

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