Seroatlas · Human Serome Atlas

PCDHAC2

Protocadherin alpha-C2

Also known as: PCDC2_HUMAN, PCDH-ALPHA-C2

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

Protein identityUniProt · HPA

UniProt accession
Q9Y5I4
Gene
PCDHAC2
Ensembl
ENSG00000243232
Chromosome
5
Canonical length
1007 aa
Protein class
Predicted membrane proteins
Subcellular location
Nucleoplasm,Mitochondria

OverviewNCBI Gene

This gene is a member of the protocadherin alpha gene cluster, one of three related gene clusters tandemly linked on chromosome five that demonstrate an unusual genomic organization similar to that of B-cell and T-cell receptor gene clusters. The alpha gene cluster is composed of 15 cadherin superfamily genes related to the mouse CNR genes and consists of 13 highly similar and 2 more distantly related coding sequences. The tandem array of 15 N-terminal exons, or variable exons, are followed by downstream C-terminal exons, or constant exons, which are shared by all genes in the cluster. The large, uninterrupted N-terminal exons each encode six cadherin ectodomains while the C-terminal exons encode the cytoplasmic domain. These neural cadherin-like cell adhesion proteins are integral plasma membrane proteins that most likely play a critical role in the establishment and function of specific cell-cell connections in the brain. Alternative splicing has been observed and additional variants have been suggested but their full-length nature has yet to be determined. [provided by RefSeq, Jul 2008]

Canonical amino-acid sequenceUniProt

1007 residues, UniProt reviewed canonical sequence.

>Q9Y5I4|PCDHAC2
     1  MEQAGTRPAA TEHPRLRRPM PWLLLLPLLL LLLLLLPGPA ASQLRYSVPE EQAPGALVGN
    61  VARALGLELR RLGPGCLRIN HLGAPSPRYL ELDLTSGALF VNERIDREAL CEQRPRCLLS
   121  LEVLAHNPVA VSAVEVEILD INDNSPRFPR PNYQLQVSES VAPGARFHIE SAQDPDVGAN
   181  SVQTYELSPS EHFELDLKPL QENSKVLELV LRKGLDREQA ALHHLVLTAV DGGIPARSGT
   241  AQISVRVLDT NDNSPAFDQS TYRVQLREDS PPGTLVVKLN ASDPDEGSNG ELRYSLSSYT
   301  SDRERQLFSI DASTGEVRVI GGLDYEEASS YQIYVQATDR GPVPMAGHCK VLVDIVDVND
   361  NAPEVVLTDL YSPVPENATP NTIVAVLSVN DQDSGPNRKV SLGLEATLPF RLNGFGNSYT
   421  LVVSGPLDRE RVAVYNITVT ATDGGIPQLT SLRTLKVEIS DINDNPPSFL EDSYSIYIQE
   481  NNLPGVLLCT VQATDPDEKE NAEVTYSLLE REIQGLPVTS YVSINSASGS LYAVNSFDYE
   541  KFREFFVTVE AQDKGSPPLS STVTANVYVV DMNDHAPHIL YPTSTNSSAA FEMVPRTAPA
   601  GYLVTKVIAM DSDSGQNAWL FYHLAQTSDL DLFKVELHTG EIRTTRKMGD ESGSTFNLTV
   661  VVRDNGEPSL SASVAITVAV VDRVSKILPD TQRHVKSPRT YSEITLYLII ALSTVSFIFL
   721  LTIIILSIIK CYRYTAYGTA CCGGFCGVRE RSPAELYKQA NNNIDARIPH GLKVQPHFIE
   781  VRGNGSLTKT YCYKACLTAG SGSDTFMFYN TGAQTGPGPS GAQAAVTDSR NLTGQSGQNA
   841  GNLIILKNEA VSQNEPRQPN PDWRYSASLR AGMHSSVHLE EAGILRAGPG GPDQQWPTVS
   901  SATPEPEAGE VSPPVGAGVN SNSWTFKYGP GNPKQSGPGE LPDKFIIPGS PAIISIRQEP
   961  TNSQIDKSDF ITFGKKEETK KKKKKKKGNK TQEKKEKGNS TTDNSDQ

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against PCDHAC2 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)
0.44
Highest tissue expression
40 nTPM

Expression across tissuesHPA

Tissue

  • parathyroid gland: 40 nTPM
  • retina: 9 nTPM
  • cerebral cortex: 7.3 nTPM
  • cerebellum: 7.1 nTPM
  • basal ganglia: 2.5 nTPM
  • gallbladder: 2.5 nTPM

Single-cell type

  • alveolar cells type 1: 1.4 nCPM
  • myosatellite cells: 1.2 nCPM
  • alveolar cells type 2: 0.9 nCPM
  • respiratory secretory cells: 0.8 nCPM
  • salivary duct cells: 0.7 nCPM
  • mesothelial cells: 0.6 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

  • midbrain: 51 nTPM
  • cerebral cortex: 29 nTPM
  • pons: 27 nTPM
  • basal ganglia: 23 nTPM
  • cerebellum: 22 nTPM
  • thalamus: 21 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)
0.34
gnomAD pLI
0.93
gnomAD missense Z
1.72
DepMap mean gene effect
0.03
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 PCDHAC2 as an antibody target. Whether an autoantibody or antibody against PCDHAC2 could matter depends on whether native PCDHAC2 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

PCDHAC2 is annotated at the cell surface, where native PCDHAC2 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 PCDHAC2 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

Canonical record: https://seroatlas.com/gene/PCDHAC2. 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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