Seroatlas · Human Serome Atlas

PCDHGA1

Protocadherin gamma-A1

Also known as: PCDG1_HUMAN, PCDH-GAMMA-A1

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

Protein identityUniProt · HPA

UniProt accession
Q9Y5H4
Gene
PCDHGA1
Ensembl
ENSG00000204956
Chromosome
5
Canonical length
931 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

931 residues, UniProt reviewed canonical sequence.

>Q9Y5H4|PCDHGA1
     1  MKIQKKLTGC SRLMLLCLSL ELLLEAGAGN IHYSVPEETD KGSFVGNIAK DLGLQPQELA
    61  DGGVRIVSRG RMPLFALNPR SGSLITARRI DREELCAQSM PCLVSFNILV EDKMKLFPVE
   121  VEIIDINDNT PQFQLEELEF KMNEITTPGT RVSLPFGQDL DVGMNSLQSY QLSSNPHFSL
   181  DVQQGADGPQ HPEMVLQSPL DREEEAVHHL ILTASDGGEP VRSGTLRIYI QVVDANDNPP
   241  AFTQAQYHIN VPENVPLGTQ LLMVNATDPD EGANGEVTYS FHNVDHRVAQ IFRLDSYTGE
   301  ISNKEPLDFE EYKMYSMEVQ AQDGAGLMAK VKVLIKVLDV NDNAPEVTIT SVTTAVPENF
   361  PPGTIIALIS VHDQDSGDNG YTTCFIPGNL PFKLEKLVDN YYRLVTERTL DRELISGYNI
   421  TITAIDQGTP ALSTETHISL LVTDINDNSP VFHQDSYSAY IPENNPRGAS IFSVRAHDLD
   481  SNENAQITYS LIEDTIQGAP LSAYLSINSD TGVLYALRSF DYEQFRDMQL KVMARDSGDP
   541  PLSSNVSLSL FLLDQNDNAP EILYPALPTD GSTGVELAPL SAEPGYLVTK VVAVDRDSGQ
   601  NAWLSYRLLK ASEPGLFSVG LHTGEVRTAR ALLDRDALKQ SLVVAVQDHG QPPLSATVTL
   661  TVAVADRISD ILADLGSLEP SAKPNDSDLT LYLVVAAAAV SCVFLAFVIV LLAHRLRRWH
   721  KSRLLQASGG GLASMPGSHF VGVDGVRAFL QTYSHEVSLT ADSRKSHLIF PQPNYADTLI
   781  SQESCEKKGF LSAPQSLLED KKEPFSQQAP PNTDWRFSQA QRPGTSGSQN GDDTGTWPNN
   841  QFDTEMLQAM ILASASEAAD GSSTLGGGAG TMGLSARYGP QFTLQHVPDY RQNVYIPGSN
   901  ATLTNAAGKR DGKAPAGGNG NKKKSGKKEK K

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against PCDHGA1 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
1.8 nTPM

Expression across tissuesHPA

Tissue

  • cerebral cortex: 1.8 nTPM
  • basal ganglia: 1.3 nTPM
  • cerebellum: 1.2 nTPM
  • heart muscle: 1.1 nTPM
  • retina: 1 nTPM
  • epididymis: 0.9 nTPM

Single-cell type

  • corticotrophs: 24 nCPM
  • lactotrophs: 21 nCPM
  • thyrotrophs: 20 nCPM
  • somatotrophs: 14 nCPM
  • sertoli cells: 14 nCPM
  • cardiomyocytes: 13 nCPM

Immune cell

  • basophil: 0.4 nTPM
  • neutrophil: 0.1 nTPM
  • NK-cell: 0.1 nTPM
  • classical monocyte: 0 nTPM
  • eosinophil: 0 nTPM
  • gdT-cell: 0 nTPM

Brain region

  • cerebellum: 10 nTPM
  • basal ganglia: 8.2 nTPM
  • hippocampal formation: 7.9 nTPM
  • cerebral cortex: 7.5 nTPM
  • spinal cord: 7 nTPM
  • medulla oblongata: 6.7 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)
0.89
gnomAD pLI
0
gnomAD missense Z
-0.05
DepMap mean gene effect
-0.08
DepMap dependency class
selective

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 PCDHGA1 as an antibody target. Whether an autoantibody or antibody against PCDHGA1 could matter depends on whether native PCDHGA1 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

PCDHGA1 is annotated at the cell surface, where native PCDHGA1 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 PCDHGA1 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

Canonical record: https://seroatlas.com/gene/PCDHGA1. 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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