Seroatlas · Human Serome Atlas

PCDHB4

Protocadherin beta-4

Also known as: PCDB4_HUMAN, PCDH-BETA4

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

Protein identityUniProt · HPA

UniProt accession: Q9Y5E5
Gene: PCDHB4
Ensembl: ENSG00000081818
Chromosome: 5
Canonical length: 795 aa
Protein class: Predicted membrane proteins
Subcellular location: Nuclear membrane,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.

>Q9Y5E5|PCDHB4
     1  MKKLGRIHPN RQVLAFILMV FLSQVRLEPI RYSVLEETES GSFVAHLAKD LGLGIGELAS
    61  RSARVLSDDD KQRLQLDRQT GDLLLREKLD REELCGPIEP CVLHFQVFLE MPVQFFQGEL
   121  LIQDINDHSP IFPEREVLLK ILENSQPGTL FPLLIAEDLD VGSNGLQKYT ISPNSHFHIL
   181  TRNHSEGKKY PDLVQDKPLD REEQPEFSLT LVALDGGSPP RSGTVMVRIL IMDINDNAPE
   241  FVHTPYGVQV LENSPLDSPI VRVLARDIDA GNFGSVSYGL FQASDEIKQT FSINEVTGEI
   301  LLKKKLDFEK IKSYHVEIEA TDGGGLSGKG TVVIEVVDVN DNPPELIISS LTSSIPENAP
   361  ETVVSIFRIR DRDSGENGKM ICSIPDNLPF ILKPTLKNFY TLVTERPLDR ETSAEYNITI
   421  AVTDLGTPRL KTQQNITVQV SDVNDNAPAF TQTSYTLFVR ENNSPALHIG SVSATDRDSG
   481  TNAQVTYSLL PPQDPHLPLA SLVSINADNG HLFALRSLDY EALQAFEFRV GASDRGSPAL
   541  SSEALVRVLV LDTNDNSPFV LYPLQNGSAP CTELVPRAAE PGYLVTKVVA VDGDSGQNAW
   601  LSYQLLKATE PGLFGVWAHN GEVRTARLLS ERDAAKHRLV VLVKDNGEPP RSATATLHVL
   661  LVDGFSQPYL PLPEAAPAQA QADSLTVYLV VALASVSSLF LFSVLLFVAV RLCRRSRAAS
   721  VGRCSVPEGP FPGHLVDVSG TGTLSQSYQY EVCLTGDSGT GEFKFLKPIF PNLLVQDTGR
   781  EVKENPKFRN SLVFS

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against PCDHB4 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: 8 nTPM

Expression across tissuesHPA

Tissue

pancreas: 8 nTPM
spinal cord: 6.9 nTPM
endometrium: 5.1 nTPM
blood vessel: 4.4 nTPM
basal ganglia: 3.9 nTPM
amygdala: 3.8 nTPM

Single-cell type

corticotrophs: 18 nCPM
breast lactating cells: 17 nCPM
oligodendrocyte progenitor cells: 14 nCPM
pancreatic acinar cells: 13 nCPM
pancreatic islet cells: 12 nCPM
respiratory ionocytes: 10 nCPM

Immune cell

T-reg: 0.2 nTPM
basophil: 0 nTPM
classical monocyte: 0 nTPM
eosinophil: 0 nTPM
gdT-cell: 0 nTPM
intermediate monocyte: 0 nTPM

Brain region

white matter: 15 nTPM
medulla oblongata: 13 nTPM
spinal cord: 12 nTPM
hypothalamus: 10 nTPM
midbrain: 9.3 nTPM
pons: 8.9 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): 1.37
gnomAD pLI: 0
gnomAD missense Z: -0.34
DepMap mean gene effect: -0.05
DepMap dependency class: none

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 PCDHB4 as an antibody target. Whether an autoantibody or antibody against PCDHB4 could matter depends on whether native PCDHB4 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

PCDHB4 is annotated at the cell surface, where native PCDHB4 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 PCDHB4 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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