Seroatlas · Human Serome Atlas

PCDHGB6

Protocadherin gamma-B6

Also known as: PCDGI_HUMAN, PCDH-GAMMA-B6

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

Protein identityUniProt · HPA

UniProt accession: Q9Y5F9
Gene: PCDHGB6
Ensembl: ENSG00000253305
Chromosome: 5
Canonical length: 930 aa
Protein class: Predicted membrane proteins
Subcellular location: Nucleoplasm,Vesicles,Plasma membrane,Cytosol

OverviewNCBI Gene

This gene is a member of the protocadherin gamma gene cluster, one of three related clusters tandemly linked on chromosome five. These gene clusters have an immunoglobulin-like organization, suggesting that a novel mechanism may be involved in their regulation and expression. The gamma gene cluster includes 22 genes divided into 3 subfamilies. Subfamily A contains 12 genes, subfamily B contains 7 genes and 2 pseudogenes, and the more distantly related subfamily C contains 3 genes. The tandem array of 22 large, variable region exons are followed by a constant region, containing 3 exons shared by all genes in the cluster. Each variable region exon encodes the extracellular region, which includes 6 cadherin ectodomains and a transmembrane region. The constant region exons encode the common cytoplasmic region. These neural cadherin-like cell adhesion proteins most likely play a critical role in the establishment and function of specific cell-cell connections in the brain. Alternative splicing has been described for the gamma cluster genes. [provided by RefSeq, Jul 2008]

Canonical amino-acid sequenceUniProt

930 residues, UniProt reviewed canonical sequence.

>Q9Y5F9|PCDHGB6
     1  MGGSCAQRRR AGPRQVLFPL LLPLFYPTLS EPIRYSIPEE LAKGSVVGNL AKDLGLSVLD
    61  VSARKLRVSA EKLHFSVDAE SGDLLVKNRI DREQICKERR RCELQLEAVV ENPLNIFHVI
   121  VVIEDVNDHA PQFDKKEIHL EIFESASAGT RLSLDPATDP DININSIKDY KINSNPYFSL
   181  MVRVNSDGGK YPELSLEKLL DREEQRSHSL ILTALDGGDP PRSATAHIEI SVKDTNDNPP
   241  VFSRDEYRIS LSENLPPGSP VLQVTATDQD EGVNAEINYY FRSTAQSTKH MFSLDEKTGM
   301  IKNNQSFDFE DVERYTMEVE AKDGGGLSTQ CKVIIEILDE NDNSPEIIIT SLSDQILENS
   361  PPGMVVALFK TRDLDFGGNG EVRCNIETDI PFKIYSSSNN YYKLVTDGAL DREQTPEYNV
   421  TIVATDRGKP PLSSSRSITL YVADINDNAP VFDQTSYVVH VAENNPPGAS IAQVSASDPD
   481  LGLNGHISYS IVASDLEPLA VSSYVSVSAQ SGVVFAQRAF DHEQLRAFAL TLQARDHGSP
   541  TLSANVSLRV LVGDRNDNAP RVLYPALGPD GSAFFDMVPR SAEPGYLVTK VVAVDADSGH
   601  NAWLSYHVLQ ASEPGLFSLG LRTGEVRTAR ALGDRDAARQ RLLVAVRDGG QPPLSATATL
   661  HLVFADNLQE ILPDLSDRPV LSDPQAELQF YLVVALALIS VLFLLAVILA IALRLRRSLS
   721  PATWDCFHPG LCVKSGPVVP PNYSEGTLPY SYNLCIAHTG TKEFNFLKCS VPLHSNEDMV
   781  CSVSPGALIP PHGGEDLTSH PETLTSQAPP NTDWRFSQAQ RPGTSGSQNG DDTGTWPNNQ
   841  FDTEMLQAMI LASASEAADG SSTLGGGAGT MGLSARYGPQ FTLQHVPDYR QNVYIPGSNA
   901  TLTNAAGKRD GKAPAGGNGN KKKSGKKEKK

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against PCDHGB6 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): 0.42
Highest tissue expression: 11 nTPM

Expression across tissuesHPA

Tissue

cerebral cortex: 11 nTPM
ovary: 4.7 nTPM
basal ganglia: 3.2 nTPM
adipose tissue: 2.9 nTPM
blood vessel: 2.9 nTPM
endometrium: 2.9 nTPM

Single-cell type

bergmann glia: 6.6 nCPM
astrocytes: 6.1 nCPM
choroid plexus epithelial cells: 5.2 nCPM
oligodendrocyte progenitor cells: 4.4 nCPM
ependymal cells: 3.5 nCPM
brain excitatory neurons: 2.8 nCPM

Immune cell

neutrophil: 0.5 nTPM
basophil: 0.3 nTPM
gdT-cell: 0.1 nTPM
memory B-cell: 0.1 nTPM
naive B-cell: 0.1 nTPM
plasmacytoid DC: 0.1 nTPM

Brain region

cerebellum: 17 nTPM
medulla oblongata: 15 nTPM
thalamus: 15 nTPM
hypothalamus: 15 nTPM
midbrain: 15 nTPM
white matter: 14 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): 0.77
gnomAD pLI: 0
gnomAD missense Z: 1.28
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

plasma membrane

Protein domainsUniProt · Pfam · InterPro

KeywordsUniProt

Antibody and autoantibody relevanceSeroatlas analysis

Seroatlas reads PCDHGB6 as an antibody target. Whether an autoantibody or antibody against PCDHGB6 could matter depends on whether native PCDHGB6 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

PCDHGB6 is annotated at the cell surface, where native PCDHGB6 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 PCDHGB6 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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