Seroatlas · Human Serome Atlas

PCDHGC4

Protocadherin gamma-C4

Also known as: PCDGL_HUMAN, PCDH-GAMMA-C4

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

Protein identityUniProt · HPA

UniProt accession: Q9Y5F7
Gene: PCDHGC4
Ensembl: ENSG00000242419
Chromosome: 5
Canonical length: 938 aa
Protein class: Disease related genes, Predicted intracellular proteins, 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

938 residues, UniProt reviewed canonical sequence.

>Q9Y5F7|PCDHGC4
     1  MLRKVRSWTE IWRWATLLFL FYHLGYVCGQ IRYPVPEESQ EGTFVGNVAQ DFLLDTDSLS
    61  ARRLQVAGEV NQRHFRVDLD SGALLIKNPI DREALCGLSA SCIVPLEFVT EGPLEMYRAE
   121  VEIVDVNDHA PRFPRQQLDL EIGEAAPPGQ RFPLEKAQDA DVGSNSISSY RLSSNEHFAL
   181  DVKKRSDGSL VPELLLEKPL DREKQSDYRL VLTAVDGGNP PRSGTAELRV SVLDVNDNAP
   241  AFQQSSYRIS VLESAPAGMV LIQLNASDPD LGPSGNVTFY FSGHTPDRVR NLFSLHPTTG
   301  KLTLLGPLDF ESENYYEFDV RARDGGSPAM EQHCSLRVDL LDVNDNAPYI TVTSELGTLP
   361  ESAEPGTVVA LISVQDPDSG SNGDVSLRIP DHLPFALKSA FRNQFSLVTA GPLDREAKSS
   421  YDIMVTASDA GNPPLSTHRT IFLNISDVND NPPSFFQRSH EVFVPENNRP GDLLCSLAAS
   481  DPDSGLNALI SYSLLEPRNR DVSASSFISL NPQTGAVHAT RSFDYEQTQT LQFEVQARDR
   541  GNPPLSSTVT VRLFVLDLND NAPAVLRPRA RPGSLCPQAL PPSVGAGHLI TKVTAVDLDS
   601  GYNAWVSYQL LEAPDPSLFA VSRYAGEVRT AVPIPADLPP QKLVIVVKDS GSPPLSTSVT
   661  LLVSLEEDTH PVVPDLRESS APREGESRLT LYLAVSLVAI CFVSFGSFVA LLSKCLRGAA
   721  CGVTCFPAGT CACLTRSRRR EGLPPSNGIL RIQLGSDDPI KFVDVGGHSH GCTPLASAPT
   781  RSDSFMMVKS PSAPMAGEPV RPSCPPSDLL YGLEQAPPNT DWRFSQAQRP GTSGSQNGDD
   841  TGTWPNNQFD TEMLQAMILA SASEAADGSS TLGGGAGTMG LSARYGPQFT LQHVPDYRQN
   901  VYIPGSNATL TNAAGKRDGK APAGGNGNKK KSGKKEKK

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against PCDHGC4 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): 0.43
Highest tissue expression: 17 nTPM

Expression across tissuesHPA

Tissue

cerebellum: 17 nTPM
cerebral cortex: 8.6 nTPM
retina: 6 nTPM
hypothalamus: 4.7 nTPM
amygdala: 2.9 nTPM
basal ganglia: 2.3 nTPM

Single-cell type

late primary spermatocytes: 0.1 nCPM
adipocytes: 0 nCPM
adrenal cortex cells: 0 nCPM
adrenal medulla cells: 0 nCPM
alveolar cells type 1: 0 nCPM
alveolar cells type 2: 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

white matter: 62 nTPM
spinal cord: 51 nTPM
midbrain: 49 nTPM
cerebellum: 45 nTPM
amygdala: 44 nTPM
thalamus: 36 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about PCDHGC4.

Disease | AllUniProt

Conditions PCDHGC4 is implicated in, by any mechanism.

Neurodevelopmental disorder with poor growth and skeletal anomalies (NEDGS) MIM:619880

Disease | GeneticClinVar

10 pathogenic / likely-pathogenic of 121 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

Neurodevelopmental disorder with poor growth and skeletal anomalies

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): 0.31
gnomAD pLI: 0.98
gnomAD missense Z: 1.97
DepMap mean gene effect: 0.08
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 PCDHGC4 as an antibody target. Whether an autoantibody or antibody against PCDHGC4 could matter depends on whether native PCDHGC4 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

PCDHGC4 is annotated at the cell surface, where native PCDHGC4 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 PCDHGC4 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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