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CDHR2 cadherin related family member 2 [ Homo sapiens (human) ]

Gene ID: 54825, updated on 26-Nov-2024

Summary

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Official Symbol
CDHR2provided by HGNC
Official Full Name
cadherin related family member 2provided by HGNC
Primary source
HGNC:HGNC:18231
See related
Ensembl:ENSG00000074276 MIM:619713; AllianceGenome:HGNC:18231
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
PCLCK; PCLKC; PCDH24
Summary
This gene is a member of the protocadherin family, which represents a subset of the larger cadherin superfamily. The members of the protocadherin family encode non-classical cadherins that function as calcium-dependent cell-cell adhesion molecules. This protocadherin represents a new candidate for tumor suppression. Alternatively spliced transcript variants that encode the same protein have been identified. [provided by RefSeq, Jan 2010]
Expression
Biased expression in duodenum (RPKM 125.9), small intestine (RPKM 110.9) and 3 other tissues See more
Orthologs
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Genomic context

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See CDHR2 in Genome Data Viewer
Location:
5q35.2
Exon count:
33
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (176542511..176595974)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (177087074..177142566)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (175969512..176022975)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124901142 Neighboring gene Fas associated factor family member 2 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:175918968-175920167 Neighboring gene MPRA-validated peak5588 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23687 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:175961121-175961790 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16654 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16655 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23688 Neighboring gene uncharacterized LOC124901143 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23689 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:175968985-175969591 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16656 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16657 Neighboring gene ring finger protein 44 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:175976615-175977548 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:175979197-175979830 Neighboring gene RNA, 7SL, cytoplasmic 684, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:175993117-175994082 Neighboring gene Sharpr-MPRA regulatory region 7457 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16658 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16659 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16660 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16661 Neighboring gene Sharpr-MPRA regulatory region 11151 Neighboring gene G protein regulated inducer of neurite outgrowth 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16662 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16663 Neighboring gene synuclein beta Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:176070445-176071086 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:176071087-176071726 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:176072308-176072818 Neighboring gene Sharpr-MPRA regulatory region 4950 Neighboring gene microRNA 4281 Neighboring gene eukaryotic translation initiation factor 4E family member 1B

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. Cadherin-related protein 24 induces morphological changes and partial cell polarization by facilitating direct cell-cell interactions. Behrendt M, et al. Biol Chem, 2012 May. PMID 22628312
  2. Differentially expressed genes between solitary large hepatocellular carcinoma and nodular hepatocellular carcinoma. Yang LY, et al. World J Gastroenterol, 2004 Dec 15. PMID 15534908, Free PMC Article
  3. Heterophilic and homophilic cadherin interactions in intestinal intermicrovillar links are species dependent. Gray ME, et al. PLoS Biol, 2021 Dec. PMID 34871294, Free PMC Article
  4. PCDH24-induced contact inhibition involves downregulation of beta-catenin signaling. Ose R, et al. Mol Oncol, 2009 Feb. PMID 19383367, Free PMC Article
  5. Protocadherin LKC, a new candidate for a tumor suppressor of colon and liver cancers, its association with contact inhibition of cell proliferation. Okazaki N, et al. Carcinogenesis, 2002 Jul. PMID 12117771

See all (20) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Heterophilic and homophilic cadherin interactions in intestinal intermicrovillar links are species dependent.
    Title: Heterophilic and homophilic cadherin interactions in intestinal intermicrovillar links are species dependent.
  2. Study found that brush border assembly is driven by the formation of Ca(2+)-dependent adhesion links between adjacent microvilli. Intermicrovillar links are composed of protocadherin-24 and mucin-like protocadherin, which target to microvillar tips and interact to form a trans-heterophilic complex.
    Title: Intestinal brush border assembly driven by protocadherin-based intermicrovillar adhesion.
  3. CDHR24 is directly involved in cell and tissue morphogenesis
    Title: Cadherin-related protein 24 induces morphological changes and partial cell polarization by facilitating direct cell-cell interactions.
  4. suppression of beta-catenin signaling by PCDH24 leads to contact inhibition
    Title: PCDH24-induced contact inhibition involves downregulation of beta-catenin signaling.
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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

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 calcium ion binding IEA
Inferred from Electronic Annotation
more info
  
enables cell adhesion molecule binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables cell adhesion molecule binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in brush border assembly IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in cell-cell adhesion mediated by cadherin IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in epithelial cell differentiation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in homophilic cell adhesion via plasma membrane adhesion molecules IEA
Inferred from Electronic Annotation
more info
  
involved_in intermicrovillar adhesion IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of cell growth involved in contact inhibition IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of microvillus length IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in anchoring junction IEA
Inferred from Electronic Annotation
more info
  
located_in apical plasma membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in brush border IDA
Inferred from Direct Assay
more info
 PubMed 
located_in brush border membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in extracellular exosome HDA PubMed 
located_in microvillus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in microvillus membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in plasma membrane IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
cadherin-related family member 2
Names
protocadherin-24

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_001171976.2 → NP_001165447.1  cadherin-related family member 2 precursor

    See identical proteins and their annotated locations for NP_001165447.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript. Both variants 1 and 2 encode the same protein.
    Source sequence(s)
    AB047004, AC091934, AK225217, AK315055
    Consensus CDS
    CCDS34297.1
    UniProtKB/Swiss-Prot
    A1L3U4, A6NC80, Q9BYE9, Q9NXP8
    Related
    ENSP00000424565.1, ENST00000510636.5
    Conserved Domains (2) summary
    cd11304
    Location:485 → 582
    Cadherin_repeat; Cadherin tandem repeat domain
    smart00112
    Location:864 → 926
    CA; Cadherin repeats

  2. NM_017675.6 → NP_060145.3  cadherin-related family member 2 precursor

    See identical proteins and their annotated locations for NP_060145.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Both variants 1 and 2 encode the same protein.
    Source sequence(s)
    AC091934
    Consensus CDS
    CCDS34297.1
    UniProtKB/Swiss-Prot
    A1L3U4, A6NC80, Q9BYE9, Q9NXP8
    Related
    ENSP00000261944.5, ENST00000261944.10
    Conserved Domains (2) summary
    cd11304
    Location:485 → 582
    Cadherin_repeat; Cadherin tandem repeat domain
    smart00112
    Location:864 → 926
    CA; Cadherin repeats

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
    176542511..176595974
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    177087074..177142566
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9BYE9.2 GenPept UniProtKB/Swiss-Prot:Q9BYE9

Gene LinkOut

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

Chemical Information
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