Seroatlas · Human Serome Atlas

PCDHGB7

Protocadherin gamma-B7

Also known as: ME6, PCDGJ_HUMAN, PCDH-GAMMA-B7

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

Protein identityUniProt · HPA

UniProt accession: Q9Y5F8
Gene: PCDHGB7
Ensembl: ENSG00000254122
Chromosome: 5
Canonical length: 929 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

929 residues, UniProt reviewed canonical sequence.

>Q9Y5F8|PCDHGB7
     1  MGGSCAQRRR AGPRQVLFPL LLPLFYPTLC EPIRYSIPEE LAKGSVVGNL AKDLGLSVLD
    61  VSARELRVSA EKLHFSVDAQ SGDLLVKDRI DREQICKERR RCELQLEAVV ENPLNIFHVI
   121  VVIEDVNDHA PQFRKDEINL EISESVSLGM GTILESAEDP DISMNSLSKY QLSPNEYFSL
   181  VEKDNPDGGK YPELVLQKTL DRETQSAHHL VLTALDGGDP PRSGTAQIRI LVIDANDNPP
   241  VFSQDVYRVS LREDVPPGTS ILRVKATDQD EGINSEITYS FFGVADKAQH VFSLDYTTGN
   301  ILTQQPLDFE EVERYTINIE AKDRGSLSTR CKVIVEVVDE NDNSPEIIIT SLSDQIMEDS
   361  PPGVVVALFK TRDQDSGENG EVRCSLSRGV PFKIHSSSNN YYKLVTDEAL DREQTPEYNV
   421  TIAATDRGKP PLSSSKTITL HITDVNDNAP VFGQSAYLVH VPENNQPGAS IAQVSASDPD
   481  FGLNGRVSYS LIASDLESRT LSSYVSVSAQ SGVVFAQRAF DHEQLRTFEL TLQARDQGSP
   541  ALSANVSLRV LVGDRNDNAP RVLYPALGPD GSALFDTVPR AAQPGYLVTK VVAVDADSGH
   601  NAWLSYHVVQ ASEPGLFSLG LRTGEVRMVR ALGDKDSVRQ RLLVAVRDGG QPPLSATATL
   661  HLVFADSLQE VLPDFSDHPT PSDSQAEMQF YLVVALALIS VLFLLAVILA IALRLRQSFS
   721  PTAGDCFESV LCSKSGPVGP PNYSEGTLPY AYNFCVPGDQ MNPEFNFFTS VDHCPATQDN
   781  LNKDSMLLAS ILTPSVEADK KILKQQAPPN TDWRFSQAQR PGTSGSQNGD DTGTWPNNQF
   841  DTEMLQAMIL ASASEAADGS STLGGGAGTM GLSARYGPQF TLQHVPDYRQ NVYIPGSNAT
   901  LTNAAGKRDG KAPAGGNGNK KKSGKKEKK

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against PCDHGB7 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: 6.9 nTPM

Expression across tissuesHPA

Tissue

ovary: 6.9 nTPM
cerebellum: 5.8 nTPM
basal ganglia: 5.7 nTPM
lung: 5.5 nTPM
endometrium: 5.3 nTPM
retina: 5.3 nTPM

Single-cell type

astrocytes: 2.5 nCPM
bergmann glia: 2.5 nCPM
choroid plexus epithelial cells: 1.9 nCPM
oligodendrocyte progenitor cells: 1.9 nCPM
ependymal cells: 1.6 nCPM
brain excitatory neurons: 1.1 nCPM

Immune cell

plasmacytoid DC: 0.1 nTPM
basophil: 0 nTPM
classical monocyte: 0 nTPM
eosinophil: 0 nTPM
gdT-cell: 0 nTPM
intermediate monocyte: 0 nTPM

Brain region

cerebellum: 32 nTPM
spinal cord: 26 nTPM
hypothalamus: 25 nTPM
white matter: 24 nTPM
medulla oblongata: 23 nTPM
midbrain: 22 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): 0.71
gnomAD pLI: 0
gnomAD missense Z: 1.03
DepMap mean gene effect: 0.13
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 PCDHGB7 as an antibody target. Whether an autoantibody or antibody against PCDHGB7 could matter depends on whether native PCDHGB7 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

PCDHGB7 is annotated at the cell surface, where native PCDHGB7 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 PCDHGB7 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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