Seroatlas · Human Serome Atlas

PCDHGB3

Protocadherin gamma-B3

Also known as: PCDGF_HUMAN, PCDH-GAMMA-B3

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

Protein identityUniProt · HPA

UniProt accession
Q9Y5G1
Gene
PCDHGB3
Ensembl
ENSG00000262209
Chromosome
5
Canonical length
929 aa
Protein class
Plasma proteins, Predicted membrane proteins
Subcellular location
Nucleoplasm,Vesicles,Plasma membrane,Cytosol

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

929 residues, UniProt reviewed canonical sequence.

>Q9Y5G1|PCDHGB3
     1  MGNSSGWRGP AGQRRMLFLF LLSLLDQALS EPIRYAIPEE LDRGSLVGNL AKDLGFGVGD
    61  LPTRNLRVIA EKKFFTVSPE NGNLLVSDRI DREEICGKKS TCVLEFEMVA EKPLNFFHVT
   121  VLIQDINDNP PTFSQNITEL EISELALTGA TFALESAQDP DVGVNSLQQY YLSPDPHFSL
   181  IQKENLDGSR YPELVLKAPL DREEQPHHHL VLTAVDGGEP SRSCTTQIRV IVADANDNPP
   241  VFTQDMYRVN VAENLPAGSS VLKVMAIDMD EGINAEIIYA FINIGKEVRQ LFKLDSKTGE
   301  LTTIGELDFE ERDSYTIGVE AKDGGHHTAY CKVQIDISDE NDNAPEITLA SESQHIQEDA
   361  ELGTAVALIK THDLDSGFNG EILCQLKGNF PFKIVQDTKN TYRLVTDGAL DREQIPEYNV
   421  TITATDKGNP PLSSSKTITL HILDVNDNVP VFHQASYTVH VAENNPPGAS IAHVRASDPD
   481  LGPNGLVSYY IVASDLEPRE LSSYVSVSAR SGVVFAQRAF DHEQLRAFEL TLQARDQGSP
   541  TLSANVSLRV LVDDRNDNAP LVLYPALGPE GSALFDMVPR SAEPGYLVTK VVAVDADSGY
   601  NAWLSYHIVQ ASEPGLFSLG LRTGEVRTAR TLGDREAARQ RLLVTVRDGG QQPLSATVML
   661  HLIFADSLQE IQPDLSDRPT PSDPQAELQF HLVVALALIS VLFLLAVILA ISLRLRCSSR
   721  PATEGYFQPG VCFKTVPGVL PTYSERTLPY SYNPCAASHS SNTEFKFLNI KAENAAPQDL
   781  LCDEASWFES NDNPEMPSNS GNLQKQAPPN TDWRFSQAQR PGTSGSQNGD DTGTWPNNQF
   841  DTEMLQAMIL ASASEAADGS STLGGGAGTM GLSARYGPQF TLQHVPDYRQ NVYIPGSNAT
   901  LTNAAGKRDG KAPAGGNGNK KKSGKKEKK

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against PCDHGB3 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
1.1 nTPM

Expression across tissuesHPA

Tissue

  • heart muscle: 1.1 nTPM
  • ovary: 1.1 nTPM
  • blood vessel: 1 nTPM
  • endometrium: 1 nTPM
  • parathyroid gland: 1 nTPM
  • cerebral cortex: 0.8 nTPM

Single-cell type

  • astrocytes: 1.1 nCPM
  • ependymal cells: 0.8 nCPM
  • bergmann glia: 0.7 nCPM
  • choroid plexus epithelial cells: 0.6 nCPM
  • oligodendrocyte progenitor cells: 0.5 nCPM
  • brain inhibitory neurons: 0.4 nCPM

Immune cell

  • basophil: 0 nTPM
  • classical monocyte: 0 nTPM
  • eosinophil: 0 nTPM
  • gdT-cell: 0 nTPM
  • intermediate monocyte: 0 nTPM
  • MAIT T-cell: 0 nTPM

Brain region

  • cerebellum: 13 nTPM
  • midbrain: 8.8 nTPM
  • medulla oblongata: 8.5 nTPM
  • white matter: 8.4 nTPM
  • cerebral cortex: 7.3 nTPM
  • basal ganglia: 7.2 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)
0.88
gnomAD pLI
0
gnomAD missense Z
-0.28
DepMap mean gene effect
-0.05
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 PCDHGB3 as an antibody target. Whether an autoantibody or antibody against PCDHGB3 could matter depends on whether native PCDHGB3 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

PCDHGB3 is annotated at the cell surface, where native PCDHGB3 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 PCDHGB3 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

Canonical record: https://seroatlas.com/gene/PCDHGB3. 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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