Seroatlas · Human Serome Atlas

PCDHGA9

Protocadherin gamma-A9

Also known as: PCDG9_HUMAN, PCDH-GAMMA-A9

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

Protein identityUniProt · HPA

UniProt accession
Q9Y5G4
Gene
PCDHGA9
Ensembl
ENSG00000261934
Chromosome
5
Canonical length
932 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

932 residues, UniProt reviewed canonical sequence.

>Q9Y5G4|PCDHGA9
     1  MAAPTKCQLR GRLVLLCSLL GMLWEARASQ IRYSVPEETE KGYIVGNISK DLALEPRELA
    61  ERRVRIVSRG RTQLFSLNPR SGTLVTAGRI DREELCAQSP RCLVNFKVLV EDRVKLYGIE
   121  IEVTDINDSA PKFQAESLEV KINEIAVPGA RYPLPEAIDP DVGVNSLQSY QLSPNHHFSL
   181  NVQTGDNGAI NPELVLERAL DREEATAHHL VLTASDGGEP RRSSTVRIHV TVLDTNDNAP
   241  VFAQRIYRVK VLENVPPGTW LLTATASDLD EGINGKVAYK FWKINEKQSL LFQLNENTGE
   301  ISTAKSLDYE ECSFYEMEIQ AEDGGGLKGW TKVLISVEDV NDNRPEVTIT SLFSPVREDA
   361  PQGTVILLFN AHDRDSGKNG QVVCSIQENL SFTLENSEED YYRLLTAQIL DREKASEYNI
   421  TVTATDRGTP PLSTEIHITL QVTDINDNPP AFSQASYSVY LPENNARGTS IFSVIAYDPD
   481  SNENSRVIYS LAEDTIQGSP LSTYVSINSD TGVLYALCSF DYEQFRDLQM QVTASDSGSP
   541  PLSSNVSLRL FVLDQNDNAP EILYPALPTD GSTGVELAPR SAEPGYLVTK VVAVDRDSGQ
   601  NAWLSYRLFK ASEPGLFSVG LHTGEVRTAR ALLDRDALKQ SLVVAVQDHG QPPLSATVTL
   661  TVAIADSIPD ILADLGSLQI PADLEASDLT LYLVVAVAVV SCVFLTFVIT LLALRLRHWH
   721  SSHLLRATSD GLAGVPTSHF VGVDGVRAFL QTYSQEFSLT ADSRKSHLIF PQPNYADTLI
   781  SQQSCEKNEP LCVSVDSKFP IEDTPLVPQA PPNTDWRFSQ AQRPGTSGSQ NGDDTGTWPN
   841  NQFDTEMLQA MILASASEAA DGSSTLGGGA GTMGLSARYG PQFTLQHVPD YRQNVYIPGS
   901  NATLTNAAGK RDGKAPAGGN GNKKKSGKKE KK

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against PCDHGA9 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
5.2 nTPM

Expression across tissuesHPA

Tissue

  • cerebral cortex: 5.2 nTPM
  • retina: 4.1 nTPM
  • cerebellum: 3.3 nTPM
  • amygdala: 3.2 nTPM
  • basal ganglia: 3 nTPM
  • ovary: 2.3 nTPM

Single-cell type

  • choroid plexus epithelial cells: 2.1 nCPM
  • oligodendrocyte progenitor cells: 1.9 nCPM
  • astrocytes: 1.7 nCPM
  • bergmann glia: 1.4 nCPM
  • ependymal cells: 1.3 nCPM
  • brain excitatory neurons: 0.8 nCPM

Immune cell

  • basophil: 0.1 nTPM
  • classical monocyte: 0 nTPM
  • eosinophil: 0 nTPM
  • gdT-cell: 0 nTPM
  • intermediate monocyte: 0 nTPM
  • MAIT T-cell: 0 nTPM

Brain region

  • cerebellum: 25 nTPM
  • white matter: 23 nTPM
  • cerebral cortex: 20 nTPM
  • medulla oblongata: 20 nTPM
  • spinal cord: 19 nTPM
  • hippocampal formation: 19 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)
0.84
gnomAD pLI
0
gnomAD missense Z
0.42
DepMap mean gene effect
-0.02
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

Protein domainsUniProt · Pfam · InterPro

KeywordsUniProt

Antibody and autoantibody relevanceSeroatlas analysis

Seroatlas reads PCDHGA9 as an antibody target. Whether an autoantibody or antibody against PCDHGA9 could matter depends on whether native PCDHGA9 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

PCDHGA9 is annotated at the cell surface, where native PCDHGA9 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 PCDHGA9 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

Canonical record: https://seroatlas.com/gene/PCDHGA9. 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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