Seroatlas · Human Serome Atlas

PCDHB8

Protocadherin beta-8

Also known as: PCDB8_HUMAN, PCDH-BETA8, PCDH3I

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

Protein identityUniProt · HPA

UniProt accession: Q9UN66
Gene: PCDHB8
Ensembl: ENSG00000120322
Chromosome: 5
Canonical length: 801 aa
Protein class: Predicted membrane proteins
Quaternary structure: Homodimer

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

801 residues, UniProt reviewed canonical sequence.

>Q9UN66|PCDHB8
     1  MEASGKLICR QRQVLFSFLL LGLSLAGAAE PRSYSVVEET EGSSFVTNLA KDLGLEQREF
    61  SRRGVRVVSR GNKLHLQLNQ ETADLLLNEK LDREDLCGHT EPCVLRFQVL LESPFEFFQA
   121  ELQVIDINDH SPVFLDKQML VKVSESSPPG TAFPLKNAED LDIGQNNIEN YIISPNSYFR
   181  VLTRKRSDGR KYPELVLDKA LDREEEAELR LTLTALDGGS PPRSGTAQVY IEVVDVNDNA
   241  PEFEQPFYRV QISEDSPISF LVVKVSATDV DTGVNGEISY SLFQASDEIS KTFKVDFLTG
   301  EIRLKKQLDF EKFQSYEVNI EARDAGGFSG KCTVLIQVID VNDHAPEVTM SAFTSPIPEN
   361  APETVVALFS VSDLDSGENG KISCSIQEDL PFLLKSSVGN FYTLLTETPL DRESRAEYNV
   421  TITVTDLGTP RLTTHLNMTV LVSDVNDNAP AFTQTSYTLF VRENNSPALH IGSVSATDRD
   481  SGTNAQVTYS LLPPQDPHLP LASLVSINTD NGHLFALRSL DYEALQAFEF RVGASDRGSP
   541  ALSSEALVRV LVLDANDNSP FVLYPLQNGS APCTELVPRA AEPGYLVTKV VAVDGDSGQN
   601  AWLSYQLLKA TEPGLFGVWA HNGEVRTARL LSERDAAKQR LVVLVKDNGE PPCSATATLH
   661  VLLVDGFSQP YLPLPEAAPA QGQADSLTVY LVVALASVSS LFLFSVLLFV AVLLCRRSRA
   721  ASVGRCSVPE GPFPGHLVDV RGTGSLSQNY QYEVCLAGGS GTNEFQLLKP VLPNIQGHSF
   781  GPEMEQNSNF RNGFGFSLQL K

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against PCDHB8 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: 1.2 nTPM

Expression across tissuesHPA

Tissue

endometrium: 1.2 nTPM
testis: 1 nTPM
blood vessel: 0.9 nTPM
parathyroid gland: 0.9 nTPM
adipose tissue: 0.8 nTPM
cerebral cortex: 0.8 nTPM

Single-cell type

distal convoluted tubule cells: 0.1 nCPM
lymphatic endothelial cells: 0.1 nCPM
renal connecting tubule cells: 0.1 nCPM
adipocytes: 0 nCPM
adrenal cortex cells: 0 nCPM
adrenal medulla cells: 0 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: 8.3 nTPM
hippocampal formation: 6.9 nTPM
white matter: 6.7 nTPM
medulla oblongata: 6.5 nTPM
thalamus: 6.3 nTPM
midbrain: 5.8 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about PCDHB8.

Disease | ImmuneIEDB

Conditions an epitope on PCDHB8 was assayed in.

lung non-small cell carcinoma T cell

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): 1.2
gnomAD pLI: 0
gnomAD missense Z: -1.75
DepMap mean gene effect: 0.12
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

plasma membrane

Protein domainsUniProt · Pfam · InterPro

KeywordsUniProt

Antibody and autoantibody relevanceSeroatlas analysis

Seroatlas reads PCDHB8 as an antibody target. Whether an autoantibody or antibody against PCDHB8 could matter depends on whether native PCDHB8 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

PCDHB8 is annotated at the cell surface, where native PCDHB8 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 PCDHB8 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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