Seroatlas · Human Serome Atlas

PCDHB2

Protocadherin beta-2

Also known as: PCDB2_HUMAN, PCDH-BETA2

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

Protein identityUniProt · HPA

UniProt accession
Q9Y5E7
Gene
PCDHB2
Ensembl
ENSG00000112852
Chromosome
5
Canonical length
798 aa
Protein class
Plasma proteins, Predicted intracellular proteins, Predicted membrane proteins
Subcellular location
Nucleoplasm

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

798 residues, UniProt reviewed canonical sequence.

>Q9Y5E7|PCDHB2
     1  MEAGEGKERV PKQRQVLIFF VLLGIAQASC QPRHYSVAEE TESGSFVANL LKDLGLEIGE
    61  LAVRGARVVS KGKKMHLQFD RQTGDLLLNE KLDREELCGP TEPCVLPFQV LLENPLQFFQ
   121  AELRIRDVND HSPVFLDKEI LLKIPESITP GTTFLIERAQ DLDVGTNSLQ NYTISPNFHF
   181  HLNLQDSLDG IILPQLVLNR ALDREEQPEI RLTLTALDGG SPPRSGTALV RIEVVDINDN
   241  VPEFAKLLYE VQIPEDSPVG SQVAIVSARD LDIGTNGEIS YAFSQASEDI RKTFRLSAKS
   301  GELLLRQKLD FESIQTYTVN IQATDGGGLS GTCVVFVQVM DLNDNPPELT MSTLINQIPE
   361  NLQDTLIAVF SVSDPDSGDN GRMVCSIQDD LPFFLKPSVE NFYTLVISTA LDRETRSEYN
   421  ITITVTDFGT PRLKTEHNIT VLVSDVNDNA PAFTQTSYTL FVRENNSPAL HIGSVSATDR
   481  DSGTNAQVTY SLLPPQDPHL PLASLVSINA DNGHLFALQS LDYEALQAFE FRVGAADRGS
   541  PALSSEALVR VLVLDANDNS PFVLYPLQNG SAPCTELVPR AAEPGYLVTK VVAVDGDSGQ
   601  NAWLSYQLLK ATEPGLFGVW AHNGEVRTAR LLRERDAAKQ RLVVLVKDNG EPPRSATATL
   661  HVLLVDGFSQ PYLLLPEAAP AQAQADLLTV YLVVALASVS SLFLFSVLLF VAVRLCRRSR
   721  AASVGRCSVP EGPFPGQMVD VSGTGTLSQS YQYEVCLTGG SGTNEFKFLK PIIPNFVAQG
   781  AERVSEANPS FRKSFEFT

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against PCDHB2 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
4.2 nTPM

Expression across tissuesHPA

Tissue

  • cerebral cortex: 4.2 nTPM
  • testis: 3.9 nTPM
  • adipose tissue: 2.5 nTPM
  • breast: 2.4 nTPM
  • colon: 2.2 nTPM
  • endometrium: 2.1 nTPM

Single-cell type

  • late primary spermatocytes: 31 nCPM
  • gastric progenitor cells: 7.7 nCPM
  • endometrial stromal cells: 5.6 nCPM
  • differentiating spermatogonia: 5.3 nCPM
  • early primary spermatocytes: 5.3 nCPM
  • decidual stromal cells: 4.5 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: 8.2 nTPM
  • hippocampal formation: 7.8 nTPM
  • white matter: 6.3 nTPM
  • basal ganglia: 5.2 nTPM
  • hypothalamus: 4.9 nTPM
  • spinal cord: 4.8 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)
1.12
gnomAD pLI
0
gnomAD missense Z
0.25
DepMap mean gene effect
-0.12
DepMap dependency class
selective

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 PCDHB2 as an antibody target. Whether an autoantibody or antibody against PCDHB2 could matter depends on whether native PCDHB2 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

PCDHB2 is annotated at the cell surface, where native PCDHB2 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 PCDHB2 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

Canonical record: https://seroatlas.com/gene/PCDHB2. 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).

© 2026 · Seroatlas, Discover Oregon LLC · Terms of use

Loading the interactive Seroatlas protein explorer...