PCDHB@

Summary

PCDHB@ (protocadherin beta cluster, HGNC:8679) is a protein-coding gene on chromosome 5q31.

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.

Source: NCBI Gene 56116 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 28 total — 1 pathogenic

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:8679
Approved symbol	PCDHB@
Name	protocadherin beta cluster
Location	5q31
Locus type	gene with protein product
Status	Approved
Aliases	PCDH3
OMIM	604967
Entrez	56116

Gene structure

Transcript identifiers

Ensembl transcripts: 0

RefSeq mRNA: 0 — MANE Select: None

Canonical transcript exons

None — 0 exons

Expression profiles

Top tissues by expression

0 total, by Bgee expression score (0-100, higher = more expressed):

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 1)

• PCDHs are candidate tumor suppressors that modulate regulatory pathways critical in development and disease, such as canonical Wnt signaling (PMID:19956686)

Cross-species orthologs

0 orthologs

Protein

Protein identifiers

Canonical reviewed UniProt: None (reviewed: )

All UniProt accessions (0):

RefSeq proteins (0): (*=MANE)

Domains & families (InterPro)

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 0 (showing top):

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

0 interactions, top by confidence (×1000):

IntAct

0 interactions, top by confidence:

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

28 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	16
Likely benign	6
Benign	5

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
1330185	GRCh37/hg19 5q31.2-31.3(chr5:139493717-140517454)x1	Pathogenic

SpliceAI

0 predictions. Top by Δscore:

AlphaMissense

0 scored. Top likely-pathogenic:

Disease associations

OMIM: gene MIM:604967 | disease phenotypes:

GenCC curated gene-disease

Mondo (1): PURA-related severe neonatal hypotonia-seizures-encephalopathy syndrome (MONDO:1060108)

Orphanet (2): PURA-related severe neonatal hypotonia-seizures-encephalopathy syndrome (Orphanet:438213), PURA-related severe neonatal hypotonia-seizures-encephalopathy syndrome due to a point mutation (Orphanet:438216)

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.