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

    Gene ID: 54825, updated on 2-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
    mouse all
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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 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)

    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

    • FLJ20124, FLJ20383, MGC163154

    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 IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    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.

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