Seroatlas · Human Serome Atlas

PCDHB3

Protocadherin beta-3

Also known as: PCDB3_HUMAN, PCDH-BETA3

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

Protein identityUniProt · HPA

UniProt accession
Q9Y5E6
Gene
PCDHB3
Ensembl
ENSG00000113205
Chromosome
5
Canonical length
796 aa
Protein class
Predicted intracellular proteins, Predicted membrane proteins
Subcellular location
Vesicles

OverviewNCBI Gene

This gene is a member of the protocadherin beta gene cluster, one of three related gene clusters tandemly linked on chromosome five. The gene clusters demonstrate an unusual genomic organization similar to that of B-cell and T-cell receptor gene clusters. The beta cluster contains 16 genes and 3 pseudogenes, each encoding 6 extracellular cadherin domains and a cytoplasmic tail that deviates from others in the cadherin superfamily. The extracellular domains interact in a homophilic manner to specify differential cell-cell connections. Unlike the alpha and gamma clusters, the transcripts from these genes are made up of only one large exon, not sharing common 3' exons as expected. These neural cadherin-like cell adhesion proteins are integral plasma membrane proteins. Their specific functions are unknown but they most likely play a critical role in the establishment and function of specific cell-cell neural connections. [provided by RefSeq, Jul 2008]

Canonical amino-acid sequenceUniProt

796 residues, UniProt reviewed canonical sequence.

>Q9Y5E6|PCDHB3
     1  MEAGGERFLR QRQVLLLFVF LGGSLAGSES RRYSVAEEKE KGFLIANLAK DLGLRVEELA
    61  ARGAQVVSKG NKQHFQLSHQ TGDLLLNEKL DREELCGPTE PCILHFQILL QNPLQFVTNE
   121  LRIIDVNDHS PVFFENEMHL KILESTLPGT VIPLGNAEDL DVGRNSLQNY TITPNSHFHV
   181  LTRSRRDGRK YPELVLDKAL DPEEQPELSL TLTALDGGSP PRSGTAQINI QVLDINDNAP
   241  EFAQPLYEVA VLENTPVNSV IVTVSASDLD TGSFGTISYA FFHASEEIRK TFQLNPITGD
   301  MQLVKYLNFE AINSYEVDIE AKDGGGLSGK STVIVQVVDV NDNPPELTLS SVNSPIPENS
   361  GETVLAVFSV SDLDSGDNGR VMCSIENNLP FFLKPSVENF YTLVSEGALD RETRSEYNIT
   421  ITITDLGTPR LKTKYNITVL VSDVNDNAPA FTQISYTLFV RENNSPALHI GSVSATDRDS
   481  GTNAQVTYSL LPPQDPHLPL SSLVSINADN GHLFALRSLD YEALQAFEFR VGATDRGSPA
   541  LSSEALVRVL VLDANDNSPF VLYPLQNGSA PCTELVPRAA EPGYLVTKVV AVDGDSGQNA
   601  WLSYQLLKAT EPGLFGVWAH NGEVRTARLL SERDAAKHRL VVLVKDNGEP PRSATATLHV
   661  LLVDGFSQPY LPLPEAAPAQ AQADLLTVYL VVALASVSSL FLFSVLLFVA VRLCRRSRAA
   721  SVGRCSVPEG PFPGQMVDVS GTGTLSQSYQ YEVCLTGGSG TNEFKFLKPI IPNFVAQGAE
   781  RVSEANPSFR KSFEFS

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against PCDHB3 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)
0.37
Highest tissue expression
3.4 nTPM

Expression across tissuesHPA

Tissue

  • testis: 3.4 nTPM
  • adipose tissue: 1.7 nTPM
  • pituitary gland: 1.7 nTPM
  • breast: 1.6 nTPM
  • parathyroid gland: 1.6 nTPM
  • endometrium: 1.4 nTPM

Single-cell type

  • corticotrophs: 7.1 nCPM
  • lactotrophs: 4.4 nCPM
  • breast myoepithelial cells: 4.3 nCPM
  • retinal pigment epithelial cells: 4.3 nCPM
  • pituitary stem cells: 2.8 nCPM
  • schwann cells: 2.7 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

  • cerebral cortex: 6.7 nTPM
  • basal ganglia: 6 nTPM
  • hippocampal formation: 5.8 nTPM
  • white matter: 5.3 nTPM
  • thalamus: 5.1 nTPM
  • cerebellum: 5 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)
1.3
gnomAD pLI
0
gnomAD missense Z
0.16
DepMap mean gene effect
0.01
DepMap dependency class
none

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 5% 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 PCDHB3 as an antibody target. Whether an autoantibody or antibody against PCDHB3 could matter depends on whether native PCDHB3 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

PCDHB3 is annotated at the cell surface, where native PCDHB3 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 PCDHB3 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

Canonical record: https://seroatlas.com/gene/PCDHB3. 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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