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PCDHGB4 protocadherin gamma subfamily B, 4 [ Homo sapiens (human) ]

Gene ID: 8641, updated on 9-Mar-2023

Summary

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Official Symbol
PCDHGB4provided by HGNC
Official Full Name
protocadherin gamma subfamily B, 4provided by HGNC
Primary source
HGNC:HGNC:8711
See related
Ensembl:ENSG00000253953 MIM:603058; AllianceGenome:HGNC:8711
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
FIB2; CDH20; PCDH-GAMMA-B4
Summary
This gene is a member of the protocadherin gamma gene cluster, one of three related clusters tandemly linked on chromosome five. These gene clusters have an immunoglobulin-like organization, suggesting that a novel mechanism may be involved in their regulation and expression. The gamma gene cluster includes 22 genes divided into 3 subfamilies. Subfamily A contains 12 genes, subfamily B contains 7 genes and 2 pseudogenes, and the more distantly related subfamily C contains 3 genes. The tandem array of 22 large, variable region exons are followed by a constant region, containing 3 exons shared by all genes in the cluster. Each variable region exon encodes the extracellular region, which includes 6 cadherin ectodomains and a transmembrane region. The constant region exons encode the common cytoplasmic region. These neural cadherin-like cell adhesion proteins most likely play a critical role in the establishment and function of specific cell-cell connections in the brain. This particular family member is expressed in fibroblasts and is thought to play a role in wound healing in response to injury. Alternative splicing has been described for the gamma cluster genes. [provided by RefSeq, Jul 2008]
Orthologs
mouse all
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Genomic context

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See PCDHGB4 in Genome Data Viewer
Location:
5q31.3
Exon count:
4
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (141387698..141512975)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (141913342..142038959)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (140767265..140892542)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene solute carrier family 25 member 2 Neighboring gene protocadherin gamma subfamily A, 1 Neighboring gene TATA-box binding protein associated factor 7 Neighboring gene protocadherin gamma cluster Neighboring gene protocadherin gamma subfamily A, 2 Neighboring gene protocadherin gamma subfamily A, 3 Neighboring gene protocadherin gamma subfamily B, 1 Neighboring gene protocadherin gamma subfamily A, 4 Neighboring gene protocadherin gamma subfamily B, 2 Neighboring gene protocadherin gamma subfamily A, 5 Neighboring gene protocadherin gamma subfamily B, 3 Neighboring gene protocadherin gamma subfamily A, 6 Neighboring gene protocadherin gamma subfamily A, 7 Neighboring gene protocadherin gamma subfamily A, 8 Neighboring gene protocadherin gamma subfamily B, 5 Neighboring gene protocadherin gamma subfamily A, 9 Neighboring gene protocadherin gamma subfamily B, 6 Neighboring gene protocadherin gamma subfamily A, 10 Neighboring gene protocadherin gamma subfamily A, 11 Neighboring gene protocadherin gamma subfamily B, 7 Neighboring gene protocadherin gamma subfamily B, 8 pseudogene Neighboring gene protocadherin gamma subfamily A, 12 Neighboring gene protocadherin gamma subfamily B, 9 pseudogene Neighboring gene RNA, 7SL, cytoplasmic 68, pseudogene Neighboring gene protocadherin gamma subfamily C, 3 Neighboring gene protocadherin gamma subfamily C, 4 Neighboring gene protocadherin gamma subfamily C, 5 Neighboring gene uncharacterized LOC124901091 Neighboring gene Sharpr-MPRA regulatory region 13534 Neighboring gene diaphanous related formin 1

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
  • 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. Multiple cadherins are expressed in human fibroblasts. Matsuyoshi N, et al. Biochem Biophys Res Commun, 1997 Jun 18. PMID 9199196
  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 (10) citations in PubMed

See citations in PubMed for homologs of this gene provided by HomoloGene

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

Clone Names

  • MGC138293, MGC142167

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables calcium ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in cell adhesion IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
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
located_in membrane NAS
Non-traceable Author Statement
more info
 PubMed 
located_in plasma membrane IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
protocadherin gamma-B4
Names
cadherin 20
fibroblast cadherin FIB2
fibroblast cadherin-2

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_000012.2 

    Range
    98082..223176
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_003736.4 → NP_003727.1  protocadherin gamma-B4 isoform 1 precursor

    See identical proteins and their annotated locations for NP_003727.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) includes the constant region exons and encodes the longest isoform (1).
    Source sequence(s)
    AC005618, AC008781
    Consensus CDS
    CCDS54928.1
    UniProtKB/Swiss-Prot
    Q9UN64, Q9UN71
    Related
    ENSP00000428288.1, ENST00000519479.2
    Conserved Domains (4) summary
    cd11304
    Location:246 → 341
    Cadherin_repeat; Cadherin tandem repeat domain
    pfam08266
    Location:32 → 112
    Cadherin_2; Cadherin-like
    pfam15974
    Location:800 → 896
    Cadherin_tail; Cadherin C-terminal cytoplasmic tail, catenin-binding region
    pfam16492
    Location:685 → 766
    Cadherin_C_2; Cadherin cytoplasmic C-terminal

  2. NM_032098.1 → NP_115269.1  protocadherin gamma-B4 isoform 2 precursor

    See identical proteins and their annotated locations for NP_115269.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) utilizes the large, first exon then continues into the downstream intron 1 sequence before terminating. This one-exon transcript encodes the shorter isoform (2).
    Source sequence(s)
    AF152520
    Consensus CDS
    CCDS75337.1
    UniProtKB/Swiss-Prot
    Q9UN71
    Related
    ENSP00000484560.1, ENST00000615384.1
    Conserved Domains (3) summary
    cd11304
    Location:246 → 341
    Cadherin_repeat; Cadherin tandem repeat domain
    pfam08266
    Location:32 → 112
    Cadherin_2; Cadherin-like
    pfam16492
    Location:685 → 766
    Cadherin_C_2; Cadherin cytoplasmic C-terminal

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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
    141387698..141512975
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    141913342..142038959
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9UN71.1 GenPept UniProtKB/Swiss-Prot:Q9UN71

Gene LinkOut

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