Seroatlas · Human Serome Atlas

PCDHGB1

Protocadherin gamma-B1

Also known as: PCDGD_HUMAN, PCDH-GAMMA-B1

Cross-references: UniProt · Ensembl · Human Protein Atlas · GeneCards · NCBI Gene

Protein identityUniProt · HPA

UniProt accession
Q9Y5G3
Gene
PCDHGB1
Ensembl
ENSG00000254221
Chromosome
5
Canonical length
927 aa
Protein class
Predicted membrane proteins
Subcellular location
Nucleoplasm,Vesicles,Plasma membrane,Focal adhesion sites,Midbody

OverviewNCBI Gene

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. Alternative splicing has been described for the gamma cluster genes. [provided by RefSeq, Jul 2008]

Canonical amino-acid sequenceUniProt

927 residues, UniProt reviewed canonical sequence.

>Q9Y5G3|PCDHGB1
     1  MQRAREAEMM KSQVLFPFLL SLFCGAISQQ IRYTIPEELA NGSRVGKLAK DLGLSVRELP
    61  TRKLRVSAED YFNVSLESGD LLVNGRIDRE KICGRKLECA LEFETVAENP MNVFHVVVVI
   121  QDINDNAPRF VAKGIDLEIC ESALPGVKFS LDSAQDADVE GNSLKLYTIN PNQYFSLSTK
   181  ESPDGSKYPV LLLEKPLDRE HQSSHRLILT AMDGGDPPLS GTTHIWIRVT DANDNAPVFS
   241  QEVYRVSLQE NVPWGTSVLR VMATDQDEGI NAEITYAFLN SPISTSLFNL NPNTGDITTN
   301  GTLDFEETSR YVLSVEAKDG GVHTAHCNVQ IEIVDENDNA PEVTFMSFSN QIPEDSDLGT
   361  VIALIKVRDK DSGQNGMVTC YTQEEVPFKL ESTSKNYYKL VIAGALNREQ TADYNVTIIA
   421  TDKGKPALSS RTSITLHISD INDNAPVFHQ ASYVVHVSEN NPPGASIAQV SASDPDLGPN
   481  GRVSYSILAS DLEPRELLSY VSVSPQSGVV FAQRAFDHEQ LRAFELTLQA RDQGSPALSA
   541  NVSLRVLVGD LNDNAPRVLY PALGPDGSAL FDMVPRAAEP GYLVTKVVAV DADSGHNAWL
   601  SYHVLQASEP GLFSLGLRTG EVRTARALGD RDAARQRLLV AVRDGGQPPL SATATLHLIF
   661  ADSLQEVLPD LSDRPEPSDP QTELQFYLVV ALALISVLFL LAVILAIALR LRRSSSLDTE
   721  GCFQTGLCSK SGPGVPPNHS EGTLPYSYNL CIASHSAKTE FNSLNLTPEM APPQDLLCDD
   781  PSMVVCASNE DHKIAYDPSL SSHQAPPNTD WRFSQAQRPG TSGSQNGDDT GTWPNNQFDT
   841  EMLQAMILAS ASEAADGSST LGGGAGTMGL SARYGPQFTL QHVPDYRQNV YIPGSNATLT
   901  NAAGKRDGKA PAGGNGNKKK SGKKEKK

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against PCDHGB1 can act on the native protein depends on physical access: surface and secreted proteins are reachable by circulating antibodies, intracellular proteins usually are not.

Antibody reachability
Cell surface
Secreted
No
Transmembrane segments
1
Mean surface accessibility (rSASA)
0.42
Highest tissue expression
12 nTPM

Expression across tissuesHPA

Tissue

  • cerebral cortex: 12 nTPM
  • parathyroid gland: 2 nTPM
  • amygdala: 1.9 nTPM
  • basal ganglia: 1.8 nTPM
  • retina: 1.5 nTPM
  • hippocampal formation: 1.3 nTPM

Single-cell type

  • bergmann glia: 1 nCPM
  • astrocytes: 0.7 nCPM
  • choroid plexus epithelial cells: 0.5 nCPM
  • ependymal cells: 0.5 nCPM
  • brain excitatory neurons: 0.3 nCPM
  • oligodendrocyte progenitor cells: 0.3 nCPM

Immune cell

  • naive CD8 T-cell: 0.1 nTPM
  • basophil: 0 nTPM
  • classical monocyte: 0 nTPM
  • eosinophil: 0 nTPM
  • gdT-cell: 0 nTPM
  • intermediate monocyte: 0 nTPM

Brain region

  • midbrain: 14 nTPM
  • white matter: 14 nTPM
  • hippocampal formation: 13 nTPM
  • medulla oblongata: 12 nTPM
  • spinal cord: 12 nTPM
  • cerebellum: 11 nTPM

Genetic constraint and essentialitygnomAD · DepMap

Does the body need this protein intact? Low LOEUF or a strong DepMap dependency means loss or blockade of the protein is likely to be felt.

gnomAD LOEUF (loss-of-function intolerance)
0.72
gnomAD pLI
0
gnomAD missense Z
0.1
DepMap mean gene effect
-0.03
DepMap dependency class
selective

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 4% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

Molecular functions

Cellular components

Protein domainsUniProt · Pfam · InterPro

KeywordsUniProt

Antibody and autoantibody relevanceSeroatlas analysis

Seroatlas reads PCDHGB1 as an antibody target. Whether an autoantibody or antibody against PCDHGB1 could matter depends on whether native PCDHGB1 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

PCDHGB1 is annotated at the cell surface, where native PCDHGB1 is exposed to circulating antibodies and is a prime autoantibody target that could block, deplete, or overstimulate it.

Annotation status

The present source text does not explicitly label PCDHGB1 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

Canonical record: https://seroatlas.com/gene/PCDHGB1. Study-independent annotations aggregated from UniProt, Human Protein Atlas, PubMed, IEDB, Pfam, InterPro, Gene Ontology, AlphaFold, gnomAD, DepMap, ClinVar, TCGA. Catalog release seroatlas-reviewed-human-uniprot-20260313.

Seroatlas is the reference for exploring autoantibody and antibody serology at the human-protein level: the autoreactome and human serome, multiplex serology (HuProt, HuScan, VirScan, PhIP-Seq).

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