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PCDHB@ protocadherin beta cluster [ Homo sapiens (human) ]

Gene ID: 56116, updated on 10-Oct-2023

Summary

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Official Symbol
PCDHB@provided by HGNC
Official Full Name
protocadherin beta clusterprovided by HGNC
Primary source
HGNC:HGNC:8679
See related
MIM:604967; AllianceGenome:HGNC:8679
Gene type
other
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
PCDH3
Summary
The protocadherin beta cluster is one of three related gene clusters tandemly linked on chromosome five. The protocadherin genes have an immunoglobulin-like genomic organization, suggesting that a novel mechanism may be involved in their regulation and expression. The beta cluster contains 16 genes and 3 pseudogenes. Each gene product contains 6 extracellular cadherin domains and a cytoplasmic tail that diverges from other cadherin superfamily members. Unlike the alpha and gamma clusters, the beta cluster has a variable region but lacks a constant region. Without this downstream region of shared exons, each transcript encodes a unique cytoplasmic tail. The specific functions of these one-exon gene products are unknown; however, they are thought to play a critical role in the establishment and function of specific cell-cell neural connections. [provided by RefSeq, Jul 2008]
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Genomic context

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See PCDHB@ in Genome Data Viewer
Location:
5q31.3
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (141051394..141248234)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (141576686..141773540)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (140430979..140627802)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene protocadherin alpha 1 Neighboring gene protocadherin alpha cluster, complex locus Neighboring gene protocadherin alpha 2 Neighboring gene protocadherin alpha 3 Neighboring gene protocadherin alpha 4 Neighboring gene protocadherin alpha 5 Neighboring gene protocadherin alpha 6 Neighboring gene protocadherin alpha 7 Neighboring gene protocadherin alpha 8 Neighboring gene protocadherin alpha 9 Neighboring gene protocadherin alpha 10 Neighboring gene protocadherin alpha 11 Neighboring gene protocadherin alpha 12 Neighboring gene protocadherin alpha 13 Neighboring gene protocadherin alpha subfamily C, 1 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:140380918-140381512 Neighboring gene protocadherin alpha subfamily C, 2 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:140382107-140382700 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:140381513-140382106 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:140383889-140384481 Neighboring gene protocadherin alpha constant Neighboring gene uncharacterized LOC124901090 Neighboring gene VISTA enhancer hs2610 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr5:140430540-140431368 Neighboring gene PCDHB1 antisense RNA 1 Neighboring gene protocadherin beta 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:140516486-140517019 Neighboring gene protocadherin beta 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:140517020-140517552 Neighboring gene protocadherin beta 3 Neighboring gene protocadherin beta 4 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:140554195-140554825 Neighboring gene protocadherin beta 5 Neighboring gene protocadherin beta 17 pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:140568148-140568708 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:140568709-140569267 Neighboring gene protocadherin beta 6 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:140573789-140574314 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:140589723-140590312 Neighboring gene protocadherin beta 7 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:140595068-140595596 Neighboring gene protocadherin beta 16 Neighboring gene protocadherin beta 8 Neighboring gene protocadherin beta 10 Neighboring gene protocadherin beta 9 Neighboring gene protocadherin beta 11 Neighboring gene protocadherin beta 12 Neighboring gene protocadherin beta 13 Neighboring gene protocadherin beta 14 Neighboring gene zinc finger protein 57 pseudogene Neighboring gene uncharacterized LOC105378199 Neighboring gene protocadherin beta 18 pseudogene Neighboring gene protocadherin beta 19 pseudogene Neighboring gene protocadherin beta 15 Neighboring gene Sharpr-MPRA regulatory region 13681 Neighboring gene solute carrier family 25 member 2

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. Frequent long-range epigenetic silencing of protocadherin gene clusters on chromosome 5q31 in Wilms' tumor. Dallosso AR, et al. PLoS Genet, 2009 Nov. PMID 19956686, Free PMC Article
  2. 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
  3. Comparative DNA sequence analysis of mouse and human protocadherin gene clusters. Wu Q, et al. Genome Res, 2001 Mar. PMID 11230163, Free PMC Article
  4. 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
  5. Large exons encoding multiple ectodomains are a characteristic feature of protocadherin genes. Wu Q, et al. Proc Natl Acad Sci U S A, 2000 Mar 28. PMID 10716726, Free PMC Article

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. PCDHs are candidate tumor suppressors that modulate regulatory pathways critical in development and disease, such as canonical Wnt signaling
    Title: Frequent long-range epigenetic silencing of protocadherin gene clusters on chromosome 5q31 in Wilms' tumor.
Submit: New GeneRIF Correction

Phenotypes

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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)

General gene information

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Markers

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
    19531..216355
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

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
    141051394..141248234
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_025791778.1 Reference GRCh38.p14 PATCHES

    Range
    286570..483410
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    141576686..141773540
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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