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    PCDH18 protocadherin 18 [ Homo sapiens (human) ]

    Gene ID: 54510, updated on 2-Nov-2024

    Summary

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    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
    mouse all
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    Genomic context

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    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

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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. PCDH18 is frequently inactivated by promoter methylation in colorectal cancer. Zhou D, et al. Sci Rep, 2017 Jun 6. PMID 28588296, Free PMC Article
    2. Search for the potential "second-hit" mechanism underlying the onset of familial hemophagocytic lymphohistiocytosis type 2 by whole-exome sequencing analysis. Gao L, et al. Transl Res, 2016 Apr. PMID 26739415
    3. Identification and characterization of three members of a novel subclass of protocadherins. Wolverton T, et al. Genomics, 2001 Aug. PMID 11549318
    4. Recent progress in protocadherin research. Suzuki ST. Exp Cell Res, 2000 Nov 25. PMID 11082270
    5. Genome-wide association study identifies a region on chromosome 11q14.3 associated with late rectal bleeding following radiation therapy for prostate cancer. Kerns SL, et al. Radiother Oncol, 2013 Jun. PMID 23719583, Free PMC Article

    See all (23) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Our results suggested that PCDH18 was a putative tumor suppressor with epigenetic silencing in colorectal cancer and a potential biomarker for colorectal cancer diagnosis.
      Title: PCDH18 is frequently inactivated by promoter methylation in colorectal cancer.
    2. A homozygous PCDH18 missense mutation (S1006L)from familial hemophagocytic lymphohistiocytosis type 2 patient destabilized the protein structure.
      Title: Search for the potential "second-hit" mechanism underlying the onset of familial hemophagocytic lymphohistiocytosis type 2 by whole-exome sequencing analysis.
    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
    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

    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

    • 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

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    Preferred Names
    protocadherin-18
    Names
    protocadherin 68-like protein

    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_001300828.2 → NP_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:470 → 572
      Cadherin_repeat; Cadherin tandem repeat domain
      cl09101
      Location:30 → 111
      E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus

    2. NM_019035.5 → NP_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:470 → 572
      Cadherin_repeat; Cadherin tandem repeat domain
      cl09101
      Location:30 → 111
      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_017008311.2 → XP_016863800.1  protocadherin-18 isoform X2

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

      See identical proteins and their annotated locations for XP_006714302.1

      Conserved Domains (2) summary
      cd11304
      Location:470 → 572
      Cadherin_repeat; Cadherin tandem repeat domain
      cl09101
      Location:30 → 111
      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_054350249.1 → XP_054206224.1  protocadherin-18 isoform X2

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

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9HCL0.3 GenPept UniProtKB/Swiss-Prot:Q9HCL0

    Gene LinkOut

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

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