Seroatlas · Human Serome Atlas

PCDHB15

Protocadherin beta-15

Also known as: PCDBF_HUMAN, PCDH-BETA15

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

Protein identityUniProt · HPA

UniProt accession: Q9Y5E8
Gene: PCDHB15
Ensembl: ENSG00000113248
Chromosome: 5
Canonical length: 787 aa
Protein class: Predicted intracellular proteins, Predicted membrane proteins
Subcellular location: Nucleoplasm,Centrosome,Basal body

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

787 residues, UniProt reviewed canonical sequence.

>Q9Y5E8|PCDHB15
     1  MEPAGERFPE QRQVLILLLL LEVTLAGWEP RRYSVMEETE RGSFVANLAN DLGLGVGELA
    61  ERGARVVSED NEQGLQLDLQ TGQLILNEKL DREKLCGPTE PCIMHFQVLL KKPLEVFRAE
   121  LLVTDINDHS PEFPEREMTL KIPETSSLGT VFPLKKARDL DVGSNNVQNY NISPNSHFHV
   181  STRTRGDGRK YPELVLDTEL DREEQAELRL TLTAVDGGSP PRSGTVQILI LVLDANDNAP
   241  EFVQALYEVQ VPENSPVGSL VVKVSARDLD TGTNGEISYS LYYSSQEIDK PFELSSLSGE
   301  IRLIKKLDFE TMSSYDLDIE ASDGGGLSGK CSVSVKVLDV NDNFPELSIS SLTSPIPENS
   361  PETEVALFRI RDRDSGENGK MICSIQDDVP FKLKPSVENF YRLVTEGALD RETRAEYNIT
   421  ITITDLGTPR LKTEQSITVL VSDVNDNAPA FTQTSYTLFV RENNSPALHI GSVSATDRDS
   481  GTNAQVTYSL LPPRDPHLPL TSLVSINTDN GHLFALQSLD YEALQAFEFR VGATDRGFPA
   541  LSSEALVRVL VLDANDNSPF VLYPLQNGSA PCTELVPRAA EPGYLVTKVV AVDGDSGQNA
   601  WLSYQLLKAT EPGLFGVWAH NGEVRTARLL SERDVAKHRL VVLVKDNGEP PRSATATLQV
   661  LLVDGFSQPY LPLPEAAPAQ AQADSLTVYL VVALASVSSL FLFSVFLFVA VRLCRRSRAA
   721  SVGRCSVPEG PFPGHLVDVS GTGTLSQSYQ YEVCLTGGSE SNDFKFLKPI FPNIVSQDSR
   781  RKSEFLE

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against PCDHB15 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: 7.1 nTPM

Expression across tissuesHPA

Tissue

ovary: 7.1 nTPM
cerebral cortex: 6.9 nTPM
endometrium: 6.4 nTPM
cervix: 6.3 nTPM
blood vessel: 5.9 nTPM
testis: 5.2 nTPM

Single-cell type

late primary spermatocytes: 12 nCPM
oligodendrocyte progenitor cells: 11 nCPM
decidual stromal cells: 9.3 nCPM
thymic myoid cells: 8.2 nCPM
early spermatids: 6.6 nCPM
corticotrophs: 6.1 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

cerebellum: 13 nTPM
medulla oblongata: 11 nTPM
midbrain: 9.3 nTPM
spinal cord: 9.3 nTPM
thalamus: 9 nTPM
white matter: 9 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): 1.35
gnomAD pLI: 0
gnomAD missense Z: -0.61
DepMap mean gene effect: -0.07
DepMap dependency class: selective

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 4% 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 PCDHB15 as an antibody target. Whether an autoantibody or antibody against PCDHB15 could matter depends on whether native PCDHB15 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

PCDHB15 is annotated at the cell surface, where native PCDHB15 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 PCDHB15 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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