Seroatlas · Human Serome Atlas

PCDHA5

Protocadherin alpha-5

Also known as: CNR6, CNRN6, CNRS6, CRNR6, PCDA5_HUMAN, PCDH-ALPHA5

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

Protein identityUniProt · HPA

UniProt accession
Q9Y5H7
Gene
PCDHA5
Ensembl
ENSG00000204965
Chromosome
5
Canonical length
936 aa
Protein class
Predicted membrane proteins
Subcellular location
Nuclear speckles,Plasma membrane,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

936 residues, UniProt reviewed canonical sequence.

>Q9Y5H7|PCDHA5
     1  MVYSRRGSLG SRLLLLWLLL AYWKAGSGQL HYSIPEEAKH GTFVGRIAQD LGLELAELVP
    61  RLFRVASKGR GDLLEVNLQN GILFVNSRID REELCRRRAE CSIHLEVIVD RPLQVFHVEV
   121  AVKDINDNPP RFSRQEQRLF ILESRMPDSR FPLEGASDLD IGANAQLRYR LNPNEYFDLD
   181  VKTNEEETNF LELVLRKSLD REETQEHRLL VIATDGGKPE LTGTVQLLIN VLDANDNAPE
   241  FDKSIYNVRL LENAPSGTLV IKLNASDADE GINKEIVYFF SNLVLDDVKS KFIINSNTGE
   301  IKVNGELDYE DYNSYEINID AMDKSTFPLS GHCKVVVKLL DVNDNTPEMA ITTLFLPVKE
   361  DAPLSTVIAL ISVSDRDSGA NGQVTCSLMP HVPFKLVSTF KNYYSLVLDS ALDRESVSVY
   421  ELVVTARDGG SPSLWATASV SVEVADVNDN APAFAQPQYT VFVKENNPPG CHIFTVSARD
   481  ADAQENALVS YSLVERRVGE RPLSSYVSVH AESGKVYALQ PLDHEEVELL QFQVSARDAG
   541  VPPLGSNVTL QVFVLDENDN APALLVPRVG GTGGAVSELV PRSVGAGHVV AKVRAVDPDS
   601  GYNAWLSYEL QPAPGSARIP FRVGLYTGEI STTRSLDETE APRHRLLVLV KDHGEPPLTA
   661  TATVLVSLVE SGQAPKASSR ASAGAVGPEA ALVDVNVYLI IAICAVSSLL VLTLLLYTAL
   721  RCSAQPTEAV CTRGKPTLLC SSAVGSWSYS QQRRQRVCSG EAPPKTDLMA FSPSLPQGPT
   781  STDNPRQPNP DWRYSASLRA GMHSSVHLEE AGILRAGPGG PDQQWPTVSS ATPEPEAGEV
   841  SPPVGAGVNS NSWTFKYGPG NPKQSGPGEL PDKFIIPGSP AIISIRQEPT NSQIDKSDFI
   901  TFGKKEETKK KKKKKKGNKT QEKKEKGNST TDNSDQ

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against PCDHA5 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
2.2 nTPM

Expression across tissuesHPA

Tissue

  • cerebellum: 2.2 nTPM
  • cerebral cortex: 1.8 nTPM
  • amygdala: 0.5 nTPM
  • hypothalamus: 0.5 nTPM
  • hippocampal formation: 0.4 nTPM
  • pituitary gland: 0.4 nTPM

Single-cell type

  • oligodendrocyte progenitor cells: 5.3 nCPM
  • bergmann glia: 3.7 nCPM
  • brain excitatory neurons: 2.8 nCPM
  • brain inhibitory neurons: 2 nCPM
  • other brain neurons: 1.3 nCPM
  • oligodendrocytes: 1.2 nCPM

Immune cell

  • basophil: 0.2 nTPM
  • neutrophil: 0.1 nTPM
  • classical monocyte: 0 nTPM
  • eosinophil: 0 nTPM
  • gdT-cell: 0 nTPM
  • intermediate monocyte: 0 nTPM

Brain region

  • cerebellum: 12 nTPM
  • cerebral cortex: 6.8 nTPM
  • basal ganglia: 6.2 nTPM
  • white matter: 5.7 nTPM
  • amygdala: 5.1 nTPM
  • hippocampal formation: 4.8 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
-0.41
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 PCDHA5 as an antibody target. Whether an autoantibody or antibody against PCDHA5 could matter depends on whether native PCDHA5 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

PCDHA5 is annotated at the cell surface, where native PCDHA5 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 PCDHA5 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

Canonical record: https://seroatlas.com/gene/PCDHA5. 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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