Seroatlas · Human Serome Atlas

PCDHB9

Protocadherin beta-9

Also known as: PCDB9_HUMAN, PCDH-BETA9, PCDH3H

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

Protein identityUniProt · HPA

UniProt accession
Q9Y5E1
Gene
PCDHB9
Ensembl
ENSG00000177839
Chromosome
5
Canonical length
797 aa
Protein class
Predicted intracellular proteins, Predicted membrane proteins

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

797 residues, UniProt reviewed canonical sequence.

>Q9Y5E1|PCDHB9
     1  MKTRGFSFPR QRQVLFLFLF WGVSLAGSGF GRYSVTEETE KGSFVVNLAK DLGLAEGELA
    61  ARGTRVVSDD NKQYLLLDSH TGNLLTNEKL DREKLCGPKE PCMLYFQILM DDPFQIYRAE
   121  LRVRDINDHS PVFRHKEMVL KISENTAEGT AFRLERAQDP DEGHNSIQNY TISSNSFFHI
   181  KISGSDEGMI YPELVLDKAL DREEQEELSL TLTALDGGSP SRSGTSTIRI VVLDVNDNVP
   241  QFAQALYETQ APENSPVGSL IVKVSAGDAD SGVNAEVSYS FFDASEDILT TFQINPFSGE
   301  IFLRELLDYE LVNSYKINIQ AMDGGGLSAR CTVLIKVLDS NDNPPELIIS SLSNSVAENS
   361  PGIVLAVFKI KDRDSGENGK TICYVQDNLP FFLKPSVDNF YILMTEGALD RESKAEYNIT
   421  ITVTDLGTPR LKTEHSITLQ VSDVNDNAPA FTQTSYTLFV RENNSPALHI GSVSATDRDS
   481  GTNAQVTYSL LPPQDPHLPL ASLVSINADN GHLFALRSLD YEALQAFDFR VGASDRGSPA
   541  LSSEALVRVL VLDANDNSPF VLYPLQNGSA PCTELVPRAA EPGYLVTKVV AVDGDSGQNA
   601  WLSYQLLKAT EPGLFGVWAH NGEVRTARLL SERDAAKHRL VVLVKDNGEP PRSATATLHV
   661  LLVDGFSQPY LPLPEAAPAQ AQADLLTVYL VVALASVSSL FLLSVLLFVA VRLCRRSRAA
   721  SVGRCSVPEG PFPGHLVDVS GTGTLFQSYQ YEVCLTGGSE TGEFKFLKPI TPHLPPHRGG
   781  KEIEENSTLP NSFGFNY

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against PCDHB9 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
4.1 nTPM

Expression across tissuesHPA

Tissue

  • cerebral cortex: 4.1 nTPM
  • pituitary gland: 2.2 nTPM
  • blood vessel: 2 nTPM
  • endometrium: 1.8 nTPM
  • epididymis: 1.7 nTPM
  • ovary: 1.7 nTPM

Single-cell type

  • adrenal medulla cells: 43 nCPM
  • retinal bipolar cells: 11 nCPM
  • sertoli cells: 9.5 nCPM
  • corticotrophs: 5.5 nCPM
  • decidual stromal cells: 5.5 nCPM
  • lactotrophs: 5.5 nCPM

Immune cell

  • basophil: 0.2 nTPM
  • memory CD8 T-cell: 0.1 nTPM
  • neutrophil: 0.1 nTPM
  • NK-cell: 0.1 nTPM
  • classical monocyte: 0 nTPM
  • eosinophil: 0 nTPM

Brain region

  • cerebral cortex: 8.3 nTPM
  • hippocampal formation: 7.5 nTPM
  • cerebellum: 6.9 nTPM
  • basal ganglia: 6.8 nTPM
  • thalamus: 6.5 nTPM
  • white matter: 6.3 nTPM

OntologyGO

Biological processes

Molecular functions

Cellular components

Protein domainsUniProt · Pfam · InterPro

KeywordsUniProt

Antibody and autoantibody relevanceSeroatlas analysis

Seroatlas reads PCDHB9 as an antibody target. Whether an autoantibody or antibody against PCDHB9 could matter depends on whether native PCDHB9 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

PCDHB9 is annotated at the cell surface, where native PCDHB9 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 PCDHB9 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

Canonical record: https://seroatlas.com/gene/PCDHB9. 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...