Seroatlas · Human Serome Atlas

PCDHB6

Protocadherin beta-6

Also known as: PCDB6_HUMAN, PCDH-BETA6

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

Protein identityUniProt · HPA

UniProt accession
Q9Y5E3
Gene
PCDHB6
Ensembl
ENSG00000113211
Chromosome
5
Canonical length
794 aa
Protein class
Predicted membrane proteins
Subcellular location
Nucleoplasm
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. Unlike the alpha and gamma clusters, the transcripts from these genes do not share common 3' exons. These neural cadherin-like cell adhesion proteins are integral plasma membrane proteins that most likely play a critical role in the establishment and function of specific cell-cell neural connections. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2014]

Canonical amino-acid sequenceUniProt

794 residues, UniProt reviewed canonical sequence.

>Q9Y5E3|PCDHB6
     1  MMQTKVQNKK RQVAFFILLM LWGEVGSESI QYSVLEETES GTFVANLTKD LGLRVGELAS
    61  RGARVVFKGN RQHLQFDPQT HDLLLNEKLD REELCGSTEP CVLPFQVLLE NPLQFFQASL
   121  RVRDINDHAP EFPAREMLLK ISEITMPGKI FPLKMAHDLD TGSNGLQRYT ISSNPHFHVL
   181  TRNRSEGRKF PELVLDKPLD REEQPQLRLT LIALDGGSPP RSGTSEIQIQ VLDINDNVPE
   241  FAQELYEAQV PENNPLGSLV ITVSARDLDA GSFGKVSYAL FQVDDVNQPF EINAITGEIR
   301  LRKALDFEEI QSYDVDVEAT DGGGLSGKCS LVVRVLDVND NAPELTMSFF ISLIPENLPE
   361  ITVAVFSVSD ADSGHNQQVI CSIENNLPFL LRPSVENFYT LVTEGALDRE SRAEYNITIT
   421  VTDLGTPRLK TQQSITVQVS DVNDNAPAFT QTSYTLFVRE NNSPALHIGS VSATDRDSGI
   481  NAQVTYSLLP PQDPHLPLSS LVSINADNGH LFALRSLDYE ALQSFEFRVG ATDRGSPALS
   541  SEALVRLLVL DANDNSPFVL YPLQNGSAPC TELVPRAAEP GYLVTKVVAV DGDSGQNAWL
   601  SYQLLKATEL GLFGVWAHNG EVRTARLLSE RDAAKHRLVV LVKDNGEPPR SATATLHVLL
   661  VDGFSQPYLP LPEAAPAQAQ ADSLTVYLVV ALASVSSLFL FSVLLFVAVR LCRRSRAASV
   721  GRYSVPEGPF PGHLVDVSGT GTLSQSYQYK VCLTGGSETN EFKFLKPIMP NFPPQGTERE
   781  MEETPTSRNS FPFS

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against PCDHB6 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
2.2 nTPM

Expression across tissuesHPA

Tissue

  • blood vessel: 2.2 nTPM
  • cerebral cortex: 1.8 nTPM
  • parathyroid gland: 1.7 nTPM
  • testis: 1.7 nTPM
  • endometrium: 1.6 nTPM
  • basal ganglia: 1.4 nTPM

Single-cell type

  • late primary spermatocytes: 26 nCPM
  • adrenal medulla cells: 11 nCPM
  • corticotrophs: 3.1 nCPM
  • early primary spermatocytes: 3.1 nCPM
  • myosatellite cells: 2.8 nCPM
  • astrocytes: 2.5 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: 5.9 nTPM
  • hippocampal formation: 5.6 nTPM
  • white matter: 5.2 nTPM
  • amygdala: 4.5 nTPM
  • medulla oblongata: 4.5 nTPM
  • thalamus: 4.4 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
-1.21
DepMap mean gene effect
0.1
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 PCDHB6 as an antibody target. Whether an autoantibody or antibody against PCDHB6 could matter depends on whether native PCDHB6 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

PCDHB6 is annotated at the cell surface, where native PCDHB6 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 PCDHB6 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

Canonical record: https://seroatlas.com/gene/PCDHB6. 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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