Seroatlas · Human Serome Atlas

PCDHB11

Protocadherin beta-11

Also known as: ME2, PCDBB_HUMAN, PCDH-BETA11

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

Protein identityUniProt · HPA

UniProt accession: Q9Y5F2
Gene: PCDHB11
Ensembl: ENSG00000197479
Chromosome: 5
Canonical length: 797 aa
Protein class: Predicted membrane proteins
Subcellular location: 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

797 residues, UniProt reviewed canonical sequence.

>Q9Y5F2|PCDHB11
     1  MENQGTRTQQ IRQVLLLFVL LGMSQAGSET WSFSVAEEMQ SGSFVGNLAK DLGLKVRELS
    61  SRGARVVSND KKQRLQLDIN TGDLLLSETL DREELCGSIE PCVLHLQVLM QNPTQFLQIE
   121  LQVRDINDHS PIFSEKQMLL EIPENSPVGA VFLLESAKDL DVGINAVKSY TISPNSHFHI
   181  KMRVIPDNRK YPELVLDKAL DYEELPELSF ILSALDGGSP PRSGTALVRV VVVDINDNSP
   241  EFEQAFYEVK IRENSILGSL ILIVSAWDLD SGTNGEICYT FSHASEDIRK TFEINQKSGE
   301  ITLRAPLDFE TIESYSIIIQ ATDGGGLFGK STVIIHVIDV NDNAPEITVS SITSPIPENT
   361  PETVVMVFSI QDIDSGDNGR IVCSIPEDLP FVLKSSVENY YTLETERPLD RESTAEYNIT
   421  ITVTDLGIPR LKTEHNTTVL VSDVNDNAPT FTQTSYTLFV RENNSPALHI GSVSATDRDS
   481  GTNAQVNYSL LPPQDLHLPL ASLVSINTDN GHLFALRSLD YEALQAFDFR VGATDRGSPA
   541  LSSEALVRVL VLDANDNSPF VLYPLQNGSA PCTELVPRAA EPGYLVTKVV AVDGDSGQNA
   601  WLSYQLLKAT EPGLFGVWAH NGEVRTARLL SERDAAKHRL VVLVKDNGEP PRSATATLQV
   661  LLVDGFSQPY LPLPEAAPAQ AQADSLTVYL VVALASVSSL FLFSVLLFVA VRLCRRSRAA
   721  SVGSCSVPKG PFPGHLVDVS GTGTLSQSYQ YEVCLTGGSE TNEFKFLKPV IPNIQAKGLG
   781  KNSEENSTFR NSFGFNF

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against PCDHB11 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: 3 nTPM

Expression across tissuesHPA

Tissue

blood vessel: 3 nTPM
pancreas: 2.5 nTPM
parathyroid gland: 2.4 nTPM
ovary: 2 nTPM
endometrium: 1.4 nTPM
adipose tissue: 1.2 nTPM

Single-cell type

retinal pigment epithelial cells: 13 nCPM
thymic myoid cells: 8.2 nCPM
corticotrophs: 5.6 nCPM
fibroblasts: 4 nCPM
endometrial secretory cells: 3.9 nCPM
pancreatic acinar cells: 3.9 nCPM

Immune cell

basophil: 0.5 nTPM
neutrophil: 0.3 nTPM
NK-cell: 0.2 nTPM
naive B-cell: 0.1 nTPM
plasmacytoid DC: 0.1 nTPM
classical monocyte: 0 nTPM

Brain region

cerebral cortex: 9.6 nTPM
cerebellum: 9 nTPM
hippocampal formation: 8.1 nTPM
white matter: 8 nTPM
midbrain: 7.9 nTPM
basal ganglia: 7.7 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): 1.59
gnomAD pLI: 0
gnomAD missense Z: -2.15
DepMap mean gene effect: -0.02
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 PCDHB11 as an antibody target. Whether an autoantibody or antibody against PCDHB11 could matter depends on whether native PCDHB11 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

PCDHB11 is annotated at the cell surface, where native PCDHB11 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 PCDHB11 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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