Seroatlas · Human Serome Atlas

PCDHB5

Protocadherin beta-5

Also known as: DKFZp586B0217, PCDB5_HUMAN, PCDH-BETA5

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

Protein identityUniProt · HPA

UniProt accession
Q9Y5E4
Gene
PCDHB5
Ensembl
ENSG00000113209
Chromosome
5
Canonical length
795 aa
Protein class
Predicted intracellular proteins, Predicted membrane proteins
Subcellular location
Vesicles,Plasma membrane

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

795 residues, UniProt reviewed canonical sequence.

>Q9Y5E4|PCDHB5
     1  METALAKTPQ KRQVMFLAIL LLLWEAGSEA VRYSIPEETE SGYSVANLAK DLGLGVGELA
    61  TRGARMHYKG NKELLQLDIK TGNLLLYEKL DREVMCGATE PCILHFQLLL ENPVQFFQTD
   121  LQLTDINDHA PEFPEKEMLL KIPESTQPGT VFPLKIAQDF DIGSNTVQNY TISPNSHFHV
   181  ATHNRGDGRK YPELVLDKAL DREERPELSL TLTALDGGAP PRSGTTTIRI VVLDNNDNAP
   241  EFLQSFYEVQ VPENSPLNSL VVVVSARDLD AGAYGSVAYA LFQGDEVTQP FVIDEKTAEI
   301  RLKRALDFEA TPYYNVEIVA TDGGGLSGKC TVAIEVVDVN DNAPELTMST LSSPTPENAP
   361  ETVVAVFSVS DPDSGDNGRM ICSIQNDLPF LLKPTLKNFY TLVTQRTLDR ESQAEYNITI
   421  TVTDMGTPRL KTEHNITVLV SDVNDNAPAF TQTSYTLFVR ENNSPALHIG SVSATDRDSG
   481  TNAQVTYSLL PPQNPHLRLA SLVSINADNG HLFALRSLDY EALQAFEFRV GATDRGSPAL
   541  SSEALVRVLV LDANDNSPFV LYPLQNGSAP CTELVPRAAE PGYLVTKVVA VDGDSGQNAW
   601  LSYQLLKATE PGLFSMWAHN GEVRTARLLS ERDAAKHRLV VLVKDNGEPP RSATATLHVL
   661  LVDGFSQPYL PLPEAAPAQA QADSLTVYLV VALASVSSLF LFSVLLFVAV RLCRRSRAAP
   721  VGRCSVPEGP FPGHLVDVSG TGTLSQSYHY EVCLTGDSGA GEFKFLKPII PNLLPQGAGE
   781  EIGKTAAFRN SFGLN

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against PCDHB5 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
6.1 nTPM

Expression across tissuesHPA

Tissue

  • ovary: 6.1 nTPM
  • pancreas: 4.4 nTPM
  • endometrium: 3.9 nTPM
  • cerebral cortex: 3.8 nTPM
  • cervix: 3.4 nTPM
  • epididymis: 3.3 nTPM

Single-cell type

  • late primary spermatocytes: 58 nCPM
  • corticotrophs: 12 nCPM
  • adrenal medulla cells: 11 nCPM
  • retinal pigment epithelial cells: 8.5 nCPM
  • early spermatids: 6.1 nCPM
  • prostatic glandular cells: 5.7 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: 13 nTPM
  • hippocampal formation: 12 nTPM
  • medulla oblongata: 12 nTPM
  • white matter: 11 nTPM
  • amygdala: 11 nTPM
  • spinal cord: 10 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
-1.12
DepMap mean gene effect
-0.01
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 PCDHB5 as an antibody target. Whether an autoantibody or antibody against PCDHB5 could matter depends on whether native PCDHB5 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

PCDHB5 is annotated at the cell surface, where native PCDHB5 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 PCDHB5 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

Canonical record: https://seroatlas.com/gene/PCDHB5. 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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