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PCDHB12 protocadherin beta 12 [ Homo sapiens (human) ]

Gene ID: 56124, updated on 2-May-2024

Summary

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Official Symbol
PCDHB12provided by HGNC
Official Full Name
protocadherin beta 12provided by HGNC
Primary source
HGNC:HGNC:8683
See related
Ensembl:ENSG00000120328 MIM:606338; AllianceGenome:HGNC:8683
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
PCDH-BETA12
Summary
This gene is a member of the protocadherin beta gene cluster, one of three related gene clusters tandemly linked on chromosome five. The gene clusters demonstrate an unusual genomic organization similar to that of B-cell and T-cell receptor gene clusters. The beta cluster contains 16 genes and 3 pseudogenes, each encoding 6 extracellular cadherin domains and a cytoplasmic tail that deviates from others in the cadherin superfamily. The extracellular domains interact in a homophilic manner to specify differential cell-cell connections. Unlike the alpha and gamma clusters, the transcripts from these genes are made up of only one large exon, not sharing common 3' exons as expected. These neural cadherin-like cell adhesion proteins are integral plasma membrane proteins. Their specific functions are unknown but they most likely play a critical role in the establishment and function of specific cell-cell neural connections. [provided by RefSeq, Jul 2008]
Orthologs
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Genomic context

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Location:
5q31.3
Exon count:
1
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (141208719..141212571)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (141734032..141737884)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (140588291..140592143)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene protocadherin beta cluster Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:140573789-140574314 Neighboring gene protocadherin beta 10 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:140589723-140590312 Neighboring gene protocadherin beta 11 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:140595068-140595596 Neighboring gene protocadherin beta 13 Neighboring gene protocadherin beta 14

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. The human and murine protocadherin-beta one-exon gene families show high evolutionary conservation, despite the difference in gene number. Vanhalst K, et al. FEBS Lett, 2001 Apr 20. PMID 11322959
  2. Phylogenetic analysis of the cadherin superfamily allows identification of six major subfamilies besides several solitary members. Nollet F, et al. J Mol Biol, 2000 Jun 9. PMID 10835267
  3. Cadherin superfamily genes: functions, genomic organization, and neurologic diversity. Yagi T, et al. Genes Dev, 2000 May 15. PMID 10817752
  4. Comparative DNA sequence analysis of mouse and human protocadherin gene clusters. Wu Q, et al. Genome Res, 2001 Mar. PMID 11230163, Free PMC Article
  5. A striking organization of a large family of human neural cadherin-like cell adhesion genes. Wu Q, et al. Cell, 1999 Jun 11. PMID 10380929

See all (14) citations in PubMed

GeneRIFs: Gene References Into Functions

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

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 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
  
involved_in nervous system development 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 beta-12
Names
PCDH-beta-12

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.

Genomic

  1. NG_000017.2 

    Range
    176844..180251
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_018932.4 → NP_061755.1  protocadherin beta-12 precursor

    See identical proteins and their annotated locations for NP_061755.1

    Status: REVIEWED

    Source sequence(s)
    AC244517, AF217746, BC045637
    Consensus CDS
    CCDS4254.1
    UniProtKB/Swiss-Prot
    B4DDU1, Q9Y5F1
    Related
    ENSP00000239450.2, ENST00000239450.4
    Conserved Domains (3) summary
    cd11304
    Location:247 → 343
    Cadherin_repeat; Cadherin tandem repeat domain
    pfam08266
    Location:35 → 112
    Cadherin_2; Cadherin-like
    pfam16492
    Location:685 → 768
    Cadherin_C_2; Cadherin cytoplasmic C-terminal

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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
    141208719..141212571
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_025791778.1 Reference GRCh38.p14 PATCHES

    Range
    443895..447747
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    141734032..141737884
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9Y5F1.1 GenPept UniProtKB/Swiss-Prot:Q9Y5F1

Gene LinkOut

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