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PCDH18 protocadherin 18 [ Homo sapiens (human) ]

Gene ID: 54510, updated on 1-Jun-2020

Summary

Official Symbol
PCDH18provided by HGNC
Official Full Name
protocadherin 18provided by HGNC
Primary source
HGNC:HGNC:14268
See related
Ensembl:ENSG00000189184 MIM:608287
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

Genomic context

See PCDH18 in Genome Data Viewer
Location:
4q28.3
Exon count:
4
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 4 NC_000004.12 (137518918..137532530, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (138440072..138453629, complement)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene ribosomal protein S23 pseudogene 2 Neighboring gene uncharacterized LOC105377442 Neighboring gene long intergenic non-protein coding RNA 2172 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

NHGRI GWAS Catalog

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • KIAA1562, DKFZp434B0923

Gene Ontology Provided by GOA

Function Evidence Code Pubs
calcium ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
brain development ISS
Inferred from Sequence or Structural Similarity
more info
 
cell adhesion IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
homophilic cell adhesion via plasma membrane adhesion molecules IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
integral component of plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
protocadherin-18
Names
protocadherin 68-like protein

NCBI Reference Sequences (RefSeq)

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/Swiss-Prot
    Q9HCL0
    UniProtKB/TrEMBL
    Q5HYG2
    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
    Q9HCL0
    UniProtKB/TrEMBL
    Q5HYG2
    Related
    ENSP00000355082.4, ENST00000344876.8
    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: Homo sapiens Updated Annotation Release 109.

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000004.12 Reference GRCh38.p13 Primary Assembly

    Range
    137518918..137532530 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

  2. XM_006714239.3XP_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
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