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    CDH22 cadherin 22 [ Homo sapiens (human) ]

    Gene ID: 64405, updated on 2-Nov-2024

    Summary

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    Official Symbol
    CDH22provided by HGNC
    Official Full Name
    cadherin 22provided by HGNC
    Primary source
    HGNC:HGNC:13251
    See related
    Ensembl:ENSG00000149654 MIM:609920; AllianceGenome:HGNC:13251
    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
    C20orf25; dJ998H6.1
    Summary
    This gene is a member of the cadherin superfamily. The gene product is composed of five cadherin repeat domains and a cytoplasmic tail similar to the highly conserved cytoplasmic region of classical cadherins. Expressed predominantly in the brain, this putative calcium-dependent cell adhesion protein may play an important role in morphogenesis and tissue formation in neural and non-neural cells during development and maintenance of the brain and neuroendocrine organs. [provided by RefSeq, Jul 2008]
    Expression
    Biased expression in brain (RPKM 3.4), skin (RPKM 1.8) and 4 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See CDH22 in Genome Data Viewer
    Location:
    20q13.12
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (46173739..46308498, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (47909792..48044527, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (44802378..44937137, complement)

    Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17960 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:44731180-44731415 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17961 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17962 Neighboring gene CRISPRi-FlowFISH-validated CD40 regulatory element GRCh37_chr20:44746135-44748232 Neighboring gene ribosomal protein L13 pseudogene 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17965 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17966 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17967 Neighboring gene CD40 molecule Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:44781551-44782092 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12973 Neighboring gene uncharacterized LOC124904916 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17968 Neighboring gene Sharpr-MPRA regulatory region 13247 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:44844486-44845022 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:44845561-44846096 Neighboring gene MPRA-validated peak4226 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:44886736-44887236 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:44928578-44929078 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:44929079-44929579 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:44932028-44932246 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:44941853-44942801 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:44952422-44952611 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:44966161-44966662 Neighboring gene Sharpr-MPRA regulatory region 3506 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:44979919-44980510 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:44980511-44981101 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:44985189-44985688 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12974 Neighboring gene uncharacterized LOC124904917 Neighboring gene solute carrier family 35 member C2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17971 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr20:45022873-45023372 Neighboring gene engulfment and cell motility 2

    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. CDH22 hypermethylation is an independent prognostic biomarker in breast cancer. Martín-Sánchez E, et al. Clin Epigenetics, 2017. PMID 28149335, Free PMC Article
    2. Expression of a novel factor, short-type PB-cadherin, in Sertoli cells and spermatogenic stem cells of the neonatal rat testis. Wu J, et al. J Endocrinol, 2003 Mar. PMID 12630923
    3. Over-expression of CDH22 is associated with tumor progression in colorectal cancer. Zhou J, et al. Tumour Biol, 2009. PMID 19546606
    4. Hypoxia activates cadherin-22 synthesis via eIF4E2 to drive cancer cell migration, invasion and adhesion. Kelly NJ, et al. Oncogene, 2018 Feb 1. PMID 28991229, Free PMC Article
    5. PRL-3 promotes epithelial mesenchymal transition by regulating cadherin directly. Liu Y, et al. Cancer Biol Ther, 2009 Jul. PMID 19440036

    See all (17) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. cadherin-22 is upregulated in hypoxia via mTORC1-independent translational control by the initiation factor eIF4E2 functioning as a hypoxia-specific cell-surface molecule involved in cancer cell migration, invasion and adhesion.
      Title: Hypoxia activates cadherin-22 synthesis via eIF4E2 to drive cancer cell migration, invasion and adhesion.
    2. Results present evidence that CDH22 is hypermethylated and its expression is downregulated in breast cancer.
      Title: CDH22 hypermethylation is an independent prognostic biomarker in breast cancer.
    3. Observational study of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Analysis of candidate genes on chromosome 20q12-13.1 reveals evidence for BMI mediated association of PREX1 with type 2 diabetes in European Americans.
    4. PRL-3 promoted downregulation of CDH22 expression.
      Title: PRL-3 promotes epithelial mesenchymal transition by regulating cadherin directly.
    5. Our results reveal for the first time a new role of CDH22 in progression of colorectal cancer.
      Title: Over-expression of CDH22 is associated with tumor progression in colorectal cancer.
    6. Observational study of gene-disease association. (HuGE Navigator)
      Title: Heterogeneity in gene loci associated with type 2 diabetes on human chromosome 20q13.1.
    7. This paper deals primarily with the rat ortholog of the human CDH22 gene.
      Title: Molecular cloning and characterization of a newly identified member of the cadherin family, PB-cadherin.
    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
    Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers.
    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

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    Knockdown of cadherin 22, type 2 (CDH22) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1 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

    Homology

    Clone Names

    • MGC39564

    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 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
    		  
    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-22
    Names
    PB-cadherin
    cadherin 22, type 2
    cadherin-like 22
    ortholog of rat PB-cadherin
    pituitary and brain cadherin

    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_021248.3 → NP_067071.1  cadherin-22 precursor

      See identical proteins and their annotated locations for NP_067071.1

      Status: REVIEWED

      Source sequence(s)
      AK289584, BC039056, BQ102264
      Consensus CDS
      CCDS13395.1
      UniProtKB/Swiss-Prot
      B9EGK7, O43205, Q9UJ99
      UniProtKB/TrEMBL
      A8K0L9
      Related
      ENSP00000437790.1, ENST00000537909.4
      Conserved Domains (2) summary
      cd11304
      Location:401 → 495
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam01049
      Location:657 → 817
      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_000020.11 Reference GRCh38.p14 Primary Assembly

      Range
      46173739..46308498 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_024451966.2 → XP_024307734.1  cadherin-22 isoform X3

      UniProtKB/TrEMBL
      A8K0L9
      Conserved Domains (3) summary
      cd11304
      Location:280 → 374
      Cadherin_repeat; Cadherin tandem repeat domain
      smart00112
      Location:3 → 45
      CA; Cadherin repeats
      pfam01049
      Location:527 → 698
      Cadherin_C; Cadherin cytoplasmic region

    2. XM_047440373.1 → XP_047296329.1  cadherin-22 isoform X2

    3. XM_011528994.3 → XP_011527296.1  cadherin-22 isoform X1

      See identical proteins and their annotated locations for XP_011527296.1

      UniProtKB/Swiss-Prot
      B9EGK7, O43205, Q9UJ99
      UniProtKB/TrEMBL
      A8K0L9
      Conserved Domains (2) summary
      cd11304
      Location:401 → 495
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam01049
      Location:657 → 817
      Cadherin_C; Cadherin cytoplasmic region

    4. XM_024451967.2 → XP_024307735.1  cadherin-22 isoform X4

      Conserved Domains (1) summary
      cd11304
      Location:172 → 253
      Cadherin_repeat; Cadherin tandem repeat domain

    5. XM_047440374.1 → XP_047296330.1  cadherin-22 isoform X5

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060944.1 Alternate T2T-CHM13v2.0

      Range
      47909792..48044527 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054323844.1 → XP_054179819.1  cadherin-22 isoform X3

    2. XM_054323843.1 → XP_054179818.1  cadherin-22 isoform X2

    3. XM_054323842.1 → XP_054179817.1  cadherin-22 isoform X1

      UniProtKB/Swiss-Prot
      B9EGK7, O43205, Q9UJ99

    4. XM_054323845.1 → XP_054179820.1  cadherin-22 isoform X4

    5. XM_054323846.1 → XP_054179821.1  cadherin-22 isoform X5

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9UJ99.2 GenPept UniProtKB/Swiss-Prot:Q9UJ99

    Gene LinkOut

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

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