Seroatlas · Human Serome Atlas

PCDHB13

Protocadherin beta-13

Also known as: PCDBD_HUMAN, PCDH-BETA13

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

Protein identityUniProt · HPA

UniProt accession
Q9Y5F0
Gene
PCDHB13
Ensembl
ENSG00000187372
Chromosome
5
Canonical length
798 aa
Protein class
Plasma 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

798 residues, UniProt reviewed canonical sequence.

>Q9Y5F0|PCDHB13
     1  MEASGKLICR QRQVLFSFLL LGLSLAGAAE PRSYSVVEET EGSSFVTNLA KDLGLEQREF
    61  SRRGVRVVSR GNKLHLQLNQ ETADLLLNEK LDREDLCGHT EPCVLRFQVL LESPFEFFQA
   121  ELQVIDINDH SPVFLDKQML VKVSESSPPG TTFPLKNAED LDVGQNNIEN YIISPNSYFR
   181  VLTRKRSDGR KYPELVLDKA LDREEEAELR LTLTALDGGS PPRSGTAQVY IEVLDVNDNA
   241  PEFEQPFYRV QISEDSPVGF LVVKVSATDV DTGVNGEISY SLFQASEEIG KTFKINPLTG
   301  EIELKKQLDF EKLQSYEVNI EARDAGTFSG KCTVLIQVID VNDHAPEVTM SAFTSPIPEN
   361  APETVVALFS VSDLDSGENG KISCSIQEDL PFLLKSAENF YTLLTERPLD RESRAEYNIT
   421  ITVTDLGTPM LITQLNMTVL IADVNDNAPA FTQTSYTLFV RENNSPALHI RSVSATDRDS
   481  GTNAQVTYSL LPPQDPHLPL TSLVSINADN GHLFALRSLD YEALQGFQFR VGASDHGSPA
   541  LSSEALVRVV VLDANDNSPF VLYPLQNGSA PCTELVPRAA EPGYLVTKVV AVDGDSGQNA
   601  WLSYQLLKAT ELGLFGVWAH NGEVRTARLL SERDAAKHRL VVLVKDNGEP PRSATATLHV
   661  LLVDGFSQPY LPLPEAAPTQ AQADLLTVYL VVALASVSSL FLFSVLLFVA VRLCRRSRAA
   721  SVGRCLVPEG PLPGHLVDMS GTRTLSQSYQ YEVCLAGGSG TNEFKFLKPI IPNFPPQCPG
   781  KEIQGNSTFP NNFGFNIQ

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against PCDHB13 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)
0.38
Highest tissue expression
1.8 nTPM

Expression across tissuesHPA

Tissue

  • pancreas: 1.8 nTPM
  • skin: 1.7 nTPM
  • blood vessel: 1.5 nTPM
  • gallbladder: 1.5 nTPM
  • endometrium: 1.4 nTPM
  • pituitary gland: 1.4 nTPM

Single-cell type

  • retinal pigment epithelial cells: 8.5 nCPM
  • corticotrophs: 8.4 nCPM
  • hepatic stellate cells: 6.5 nCPM
  • pituitary stem cells: 5.6 nCPM
  • lactotrophs: 5.4 nCPM
  • salivary ionocytes: 4.7 nCPM

Immune cell

  • neutrophil: 2.9 nTPM
  • basophil: 0.9 nTPM
  • eosinophil: 0.8 nTPM
  • naive B-cell: 0.4 nTPM
  • memory B-cell: 0.3 nTPM
  • classical monocyte: 0.2 nTPM

Brain region

  • cerebral cortex: 12 nTPM
  • cerebellum: 10 nTPM
  • hippocampal formation: 10 nTPM
  • white matter: 10 nTPM
  • basal ganglia: 9.8 nTPM
  • amygdala: 9.5 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)
1.75
gnomAD pLI
0
gnomAD missense Z
-1.92
DepMap mean gene effect
0.09
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 PCDHB13 as an antibody target. Whether an autoantibody or antibody against PCDHB13 could matter depends on whether native PCDHB13 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

PCDHB13 is annotated at the cell surface, where native PCDHB13 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 PCDHB13 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

Canonical record: https://seroatlas.com/gene/PCDHB13. 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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