Seroatlas · Human Serome Atlas

PCDHA2

Protocadherin alpha-2

Also known as: PCDA2_HUMAN

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

Protein identityUniProt · HPA

UniProt accession
Q9Y5H9
Gene
PCDHA2
Ensembl
ENSG00000204969
Chromosome
5
Canonical length
948 aa
Protein class
Predicted membrane proteins

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

948 residues, UniProt reviewed canonical sequence.

>Q9Y5H9|PCDHA2
     1  MASSIRRGRG AWTRLLSLLL LAAWEVGSGQ LRYSVPEEAK HGTFVGRIAQ DLGLELEELV
    61  PRLFRVASKR HGDLLEVNLQ NGILFVNSRI DREELCGRSA ECSIHVEVIV DRPLQVFHVE
   121  VEVKDINDNP PIFPMTVKTI RFPESRLLDS RFPLEGASDA DIGVNALLSY KLSSSEFFFL
   181  DIQANDELSE SLSLVLGKSL DREETAEVNL LLVATDGGKP ELTGTVQILI KVLDVNDNEP
   241  TFAQSVYKVK LLENTANGTL VVKLNASDAD EGPNSEIVYS LGSDVSSTIQ TKFTIDPISG
   301  EIRTKGKLDY EEAKSYEIQV TATDKGTPSM SGHCKISLKL VDINDNTPEV SITSLSLPIS
   361  ENASLGTVIA LITVSDRDSG TNGHVTCSLT PHVPFKLVST FKNYYSLVLD SALDRESVSA
   421  YELVVTARDG GSPSLWATTS VSIEVADVND NAPAFAQPEY TVFVKENNPP GCHIFTVSAW
   481  DADAQENALV SYSLVERRVG ERALSSYVSV HAESGKVYAL QPLDHEEVEL LQFQVSARDA
   541  GVPPLGSNVT LQVFVLDEND NAPALLAPRA GTAAGAVSEL VPWSVGAGHV VAKVRAVDAD
   601  SGYNAWLSYE LQLGTGSARI PFRVGLYTGE ISTTRALDEA DSPRHRLLVL VKDHGEPALT
   661  ATATVLVSLV ESGQAPKASS RAWVGAAGSE ATLVDVNVYL IIAICAVSSL LVLTVLLYTA
   721  LRCSVPPTEG ARAPGKPTLV CSSAVGSWSY SQQRRQRVCS GEDPPKTDLM AFSPSLSQGP
   781  DSAEEKQLSE SEYVGKPRQP NPDWRYSASL RAGMHSSVHL EEAGILRAGP GGPDQQWPTV
   841  SSATPEPEAG EVSPPVGAGV NSNSWTFKYG PGNPKQSGPG ELPDKFIIPG SPAIISIRQE
   901  PTNSQIDKSD FITFGKKEET KKKKKKKKGN KTQEKKEKGN STTDNSDQ

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against PCDHA2 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
2.1 nTPM

Expression across tissuesHPA

Tissue

  • cerebellum: 2.1 nTPM
  • pituitary gland: 1.4 nTPM
  • testis: 0.8 nTPM
  • amygdala: 0.5 nTPM
  • cerebral cortex: 0.5 nTPM
  • retina: 0.5 nTPM

Single-cell type

  • oligodendrocyte progenitor cells: 1 nCPM
  • bergmann glia: 0.3 nCPM
  • early spermatids: 0.3 nCPM
  • brain excitatory neurons: 0.2 nCPM
  • brain inhibitory neurons: 0.2 nCPM
  • other brain neurons: 0.2 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

  • cerebellum: 5.8 nTPM
  • medulla oblongata: 3.7 nTPM
  • white matter: 3.6 nTPM
  • pons: 3.3 nTPM
  • basal ganglia: 3.1 nTPM
  • spinal cord: 2.9 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)
1.51
gnomAD pLI
0
gnomAD missense Z
-0.74
DepMap mean gene effect
-0.11
DepMap dependency class
selective

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 PCDHA2 as an antibody target. Whether an autoantibody or antibody against PCDHA2 could matter depends on whether native PCDHA2 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

PCDHA2 is annotated at the cell surface, where native PCDHA2 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 PCDHA2 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

Canonical record: https://seroatlas.com/gene/PCDHA2. 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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