Seroatlas · Human Serome Atlas

PCDHA1

Protocadherin alpha-1

Also known as: PCDA1_HUMAN

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

Protein identityUniProt · HPA

UniProt accession
Q9Y5I3
Gene
PCDHA1
Ensembl
ENSG00000204970
Chromosome
5
Canonical length
950 aa
Protein class
Predicted membrane proteins, Predicted secreted proteins
Subcellular location
Endoplasmic reticulum,Golgi apparatus,Plasma membrane
Secretome location
Secreted - unknown location

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

950 residues, UniProt reviewed canonical sequence.

>Q9Y5I3|PCDHA1
     1  MVFSRRGGLG ARDLLLWLLL LAAWEVGSGQ LHYSIPEEAK HGTFVGRVAQ DLGLELAELV
    61  PRLFRVASKT HRDLLEVNLQ NGILFVNSRI DREELCQWSA ECSIHLELIA DRPLQVFHVE
   121  VKVKDINDNP PVFRGREQII FIPESRLLNS RFPIEGAADA DIGANALLTY TLSPSDYFSL
   181  DVEASDELSK SLWLELRKYL DREETPELHL LLTATDGGKP ELQGTVELLI TVLDVNDNAP
   241  LFDQAVYRVH LLETTANGTL VTTLNASDAD EGVNGEVVFS FDSGISRDIQ EKFKVDSSSG
   301  EIRLIDKLDY EETKSYEIQV KAVDKGSPPM SNHCKVLVKV LDVNDNAPEL AVTSLYLPIR
   361  EDAPLSTVIA LITVSDRDSG ANGQVTCSLM PHVPFKLVST FKNYYSLVLD SALDRESLSV
   421  YELVVTARDG GSPSLWATAR VSVEVADVND NAPAFAQPEY TVFVKENNPP GCHIFTVSAR
   481  DADAQENALV SYSLVERRVG ERALSNYVSV HAESGKVYAL QPLDHEELEL LQFQVSARDA
   541  GVPPLGSNVT LQVFVLDEND NAPALLAPRV GGTIGAVSEL VPRLVGAGHV VAKVRAVDAD
   601  SGYNAWLSYE LQPAAGGARI PFRVGLYTGE ISTTRVLDEA DLSRYRLLVL VKDHGEPALT
   661  ATATVLVSLV ESGQAPKASS RASVGVAGPE AALVDVNVYL IIAICAVSSL LVLTLLLYTA
   721  LRCSVPPTEG AYVPGKPTLV CSSALGSWSN SQQRRQRVCS SEGPPKTDLM AFSPGLSPSL
   781  NTSERNEQPE ANLDLSGNPR QPNPDWRYSA SLRAGMHSSV HLEEAGILRA GPGGPDQQWP
   841  TVSSATPEPE AGEVSPPVGA GVNSNSWTFK YGPGNPKQSG PGELPDKFII PGSPAIISIR
   901  QEPTNSQIDK SDFITFGKKE ETKKKKKKKK GNKTQEKKEK GNSTTDNSDQ

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against PCDHA1 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
1.9 nTPM

Expression across tissuesHPA

Tissue

  • spinal cord: 1.9 nTPM
  • cerebellum: 1.3 nTPM
  • cerebral cortex: 1.3 nTPM
  • basal ganglia: 1.2 nTPM
  • hippocampal formation: 1 nTPM
  • amygdala: 0.9 nTPM

Single-cell type

  • early spermatids: 5.1 nCPM
  • lactotrophs: 3.4 nCPM
  • oligodendrocyte progenitor cells: 2.6 nCPM
  • pancreatic islet cells: 2.6 nCPM
  • bergmann glia: 2.2 nCPM
  • early primary spermatocytes: 2.2 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: 6.3 nTPM
  • medulla oblongata: 5.9 nTPM
  • cerebellum: 5.5 nTPM
  • pons: 4.8 nTPM
  • cerebral cortex: 4.5 nTPM
  • spinal cord: 4.4 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)
0.88
gnomAD pLI
0
gnomAD missense Z
-0.33
DepMap mean gene effect
-0.07
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 PCDHA1 as an antibody target. Whether an autoantibody or antibody against PCDHA1 could matter depends on whether native PCDHA1 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

PCDHA1 is annotated at the cell surface, where native PCDHA1 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 PCDHA1 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

Canonical record: https://seroatlas.com/gene/PCDHA1. 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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