Seroatlas · Human Serome Atlas

PCDH9

Protocadherin-9

Also known as: PCDH9_HUMAN

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

Protein identityUniProt · HPA

UniProt accession
Q9HC56
Gene
PCDH9
Ensembl
ENSG00000184226
Chromosome
13
Canonical length
1237 aa
Protein class
Plasma proteins, Predicted membrane proteins
Subcellular location
Nucleoplasm,Centrosome

OverviewNCBI Gene

This gene encodes a member of the protocadherin family, and cadherin superfamily, of transmembrane proteins containing cadherin domains. These proteins mediate cell adhesion in neural tissues in the presence of calcium. The encoded protein may be involved in signaling at neuronal synaptic junctions. Sharing a characteristic with other protocadherin genes, this gene has a notably large exon that encodes multiple cadherin domains and a transmembrane region. Alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, Nov 2012]

Canonical amino-acid sequenceUniProt

1237 residues, UniProt reviewed canonical sequence.

>Q9HC56|PCDH9
     1  MDLRDFYLLA ALIACLRLDS AIAQELIYTI REELPENVPI GNIPKDLNIS HINAATGTSA
    61  SLVYRLVSKA GDAPLVKVSS STGEIFTTSN RIDREKLCAG ASYAEENECF FELEVVILPN
   121  DFFRLIKIKI IVKDTNDNAP MFPSPVINIS IPENTLINSR FPIPSATDPD TGFNGVQHYE
   181  LLNGQSVFGL DIVETPEGEK WPQLIVQQNL DREQKDTYVM KIKVEDGGTP QKSSTAILQV
   241  TVSDVNDNRP VFKEGQVEVH IPENAPVGTS VIQLHATDAD IGSNAEIRYI FGAQVAPATK
   301  RLFALNNTTG LITVQRSLDR EETAIHKVTV LASDGSSTPA RATVTINVTD VNDNPPNIDL
   361  RYIISPINGT VYLSEKDPVN TKIALITVSD KDTDVNGKVI CFIEREVPFH LKAVYDNQYL
   421  LETSSLLDYE GTKEFSFKIV ASDSGKPSLN QTALVRVKLE DENDNPPIFN QPVIELSVSE
   481  NNRRGLYLTT ISATDEDSGK NADIVYQLGP NASFFDLDRK TGVLTASRVF DREEQERFIF
   541  TVTARDNGTP PLQSQAAVIV TVLDENDNSP KFTHNHFQFF VSENLPKYST VGVITVTDAD
   601  AGENKAVTLS ILNDNDNFVL DPYSGVIKSN VSFDREQQSS YTFDVKATDG GQPPRSSTAK
   661  VTINVMDVND NSPVVISPPS NTSFKLVPLS AIPGSVVAEV FAVDVDTGMN AELKYTIVSG
   721  NNKGLFRIDP VTGNITLEEK PAPTDVGLHR LVVNISDLGY PKSLHTLVLV FLYVNDTAGN
   781  ASYIYDLIRR TMETPLDRNI GDSSQPYQNE DYLTIMIAII AGAMVVIVVI FVTVLVRCRH
   841  ASRFKAAQRS KQGAEWMSPN QENKQNKKKK RKKRKSPKSS LLNFVTIEES KPDDAVHEPI
   901  NGTISLPAEL EEQSIGRFDW GPAPPTTFKP NSPDLAKHYK SASPQPAFHL KPDTPVSVKK
   961  HHVIQELPLD NTFVGGCDTL SKRSSTSSDH FSASECSSQG GFKTKGPLHT RQCNSHSKSD
  1021  NIPVTPQKCP SSTGFHIQEN EESHYESQRR VTFHLPDGSQ ESCSDSGLGD HEPVGSGTLI
  1081  SHPLPLVQPQ DEFYDQASPD KRTEADGNSD PNSDGPLGPR GLAEATEMCT QECLVLGHSD
  1141  NCWMPPGLGP YQHPKSPLST FAPQKEWVKK DKLVNGHTLT RAWKEDSNRN QFNDRKQYGS
  1201  NEGHFNNGSH MTDIPLANLK SYKQAGGATE SPKEHQL

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against PCDH9 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)
0.46
Highest tissue expression
38 nTPM

Expression across tissuesHPA

Tissue

  • cerebral cortex: 38 nTPM
  • midbrain: 21 nTPM
  • amygdala: 20 nTPM
  • hippocampal formation: 20 nTPM
  • spinal cord: 19 nTPM
  • basal ganglia: 19 nTPM

Single-cell type

  • oligodendrocytes: 13,244 nCPM
  • bergmann glia: 9,746 nCPM
  • oligodendrocyte progenitor cells: 7,818 nCPM
  • astrocytes: 6,655 nCPM
  • brain excitatory neurons: 3,138 nCPM
  • retinal ganglion cells: 3,001 nCPM

Immune cell

  • naive B-cell: 17 nTPM
  • memory B-cell: 5.3 nTPM
  • basophil: 4.5 nTPM
  • plasmacytoid DC: 1.2 nTPM
  • NK-cell: 0.9 nTPM
  • total PBMC: 0.2 nTPM

Brain region

  • white matter: 441 nTPM
  • basal ganglia: 295 nTPM
  • thalamus: 282 nTPM
  • pons: 242 nTPM
  • cerebral cortex: 238 nTPM
  • medulla oblongata: 235 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)
0.37
gnomAD pLI
0.81
gnomAD missense Z
2.33
DepMap mean gene effect
0.03
DepMap dependency class
none

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 3% 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 PCDH9 as an antibody target. Whether an autoantibody or antibody against PCDH9 could matter depends on whether native PCDH9 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

PCDH9 is annotated at the cell surface, where native PCDH9 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 PCDH9 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

Canonical record: https://seroatlas.com/gene/PCDH9. 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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