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    PCDH18 protocadherin 18 [ Homo sapiens (human) ]

    Gene ID: 54510, updated on 9-Dec-2024

    Summary

    Official Symbol
    PCDH18provided by HGNC
    Official Full Name
    protocadherin 18provided by HGNC
    Primary source
    HGNC:HGNC:14268
    See related
    Ensembl:ENSG00000189184 MIM:608287; AllianceGenome:HGNC:14268
    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
    PCDH68L
    Summary
    This gene belongs to the protocadherin gene family, a subfamily of the cadherin superfamily. This gene encodes a protein which contains 6 extracellular cadherin domains, a transmembrane domain and a cytoplasmic tail differing from those of the classical cadherins. Although its specific function is undetermined, the cadherin-related neuronal receptor is thought to play a role in the establishment and function of specific cell-cell connections in the brain. [provided by RefSeq, Jul 2008]
    Expression
    Broad expression in placenta (RPKM 18.1), endometrium (RPKM 17.7) and 21 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See PCDH18 in Genome Data Viewer
    Location:
    4q28.3
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (137518918..137532494, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (140842322..140855898, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (138440072..138453648, complement)

    Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene ribosomal protein S23 pseudogene 2 Neighboring gene uncharacterized LOC105377442 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:138417700-138418253 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21908 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:138458683-138459528 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:138464138-138465055 Neighboring gene long intergenic non-protein coding RNA 2172 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21909 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:138494055-138494554 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:138553021-138553521 Neighboring gene uncharacterized LOC101927414 Neighboring gene uncharacterized LOC107986314

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    EBI GWAS Catalog

    Description
    A genome-wide meta-analysis of association studies of Cloninger's Temperament Scales.
    EBI GWAS Catalog
    Genome-wide association study identifies a region on chromosome 11q14.3 associated with late rectal bleeding following radiation therapy for prostate cancer.
    EBI GWAS Catalog
    Genome-wide association study of retinopathy in individuals without diabetes.
    EBI GWAS Catalog
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
    EBI GWAS Catalog

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • KIAA1562, DKFZp434B0923

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables calcium ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in brain development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in cell adhesion 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 plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     

    General protein information

    Preferred Names
    protocadherin-18
    Names
    protocadherin 68-like protein

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001300828.2NP_001287757.1  protocadherin-18 isoform 2 precursor

      See identical proteins and their annotated locations for NP_001287757.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the central coding region, compared to variant 1. The encoded isoform (2) is shorter, compared to isoform 1.
      Source sequence(s)
      AB046782, AK292018, BG541979, BQ017212, BX097655, BX647786
      Consensus CDS
      CCDS75193.1
      UniProtKB/TrEMBL
      D6RIG4
      Related
      ENSP00000390688.2, ENST00000412923.6
      Conserved Domains (2) summary
      cd11304
      Location:470572
      Cadherin_repeat; Cadherin tandem repeat domain
      cl09101
      Location:30111
      E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus
    2. NM_019035.5NP_061908.1  protocadherin-18 isoform 1 precursor

      See identical proteins and their annotated locations for NP_061908.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AB046782, BG541979, BQ017212, BX097655, BX647786
      Consensus CDS
      CCDS34064.1
      UniProtKB/Swiss-Prot
      A8K7K3, B7ZKT1, Q52LS2, Q9HCL0
      UniProtKB/TrEMBL
      D6RIG4
      Related
      ENSP00000355082.4, ENST00000344876.9
      Conserved Domains (2) summary
      cd11304
      Location:470572
      Cadherin_repeat; Cadherin tandem repeat domain
      cl09101
      Location:30111
      E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus

    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_000004.12 Reference GRCh38.p14 Primary Assembly

      Range
      137518918..137532494 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017008311.2XP_016863800.1  protocadherin-18 isoform X2

    2. XM_006714239.4XP_006714302.1  protocadherin-18 isoform X1

      See identical proteins and their annotated locations for XP_006714302.1

      Conserved Domains (2) summary
      cd11304
      Location:470572
      Cadherin_repeat; Cadherin tandem repeat domain
      cl09101
      Location:30111
      E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060928.1 Alternate T2T-CHM13v2.0

      Range
      140842322..140855898 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054350249.1XP_054206224.1  protocadherin-18 isoform X2

    2. XM_054350248.1XP_054206223.1  protocadherin-18 isoform X1