Seroatlas · Human Serome Atlas

PCDH19

Protocadherin-19

Also known as: EFMR, EIEE9, KIAA1313, PCD19_HUMAN

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

Protein identityUniProt · HPA

UniProt accession
Q8TAB3
Gene
PCDH19
Ensembl
ENSG00000165194
Chromosome
X
Canonical length
1148 aa
Protein class
Disease related genes, Human disease related genes, Predicted intracellular proteins, Predicted membrane proteins
Subcellular location
Cytosol
Quaternary structure
Homodimer

OverviewNCBI Gene

The protein encoded by this gene is a member of the delta-2 protocadherin subclass of the cadherin superfamily. The encoded protein is thought to be a calcium-dependent cell-adhesion protein that is primarily expressed in the brain. Mutations in this gene on human chromosome X are associated with sporadic infantile epileptic encephalopathy and to a female-restricted form of epilepsy (EFMR; also known as PCDH19RE). Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2017]

Canonical amino-acid sequenceUniProt

1148 residues, UniProt reviewed canonical sequence.

>Q8TAB3|PCDH19
     1  MESLLLPVLL LLAILWTQAA ALINLKYSVE EEQRAGTVIA NVAKDAREAG FALDPRQASA
    61  FRVVSNSAPH LVDINPSSGL LVTKQKIDRD LLCRQSPKCI ISLEVMSSSM EICVIKVEIK
   121  DLNDNAPSFP AAQIELEISE AASPGTRIPL DSAYDPDSGS FGVQTYELTP NELFGLEIKT
   181  RGDGSRFAEL VVEKSLDRET QSHYSFRITA LDGGDPPRLG TVGLSIKVTD SNDNNPVFSE
   241  STYAVSVPEN SPPNTPVIRL NASDPDEGTN GQVVYSFYGY VNDRTRELFQ IDPHSGLVTV
   301  TGALDYEEGH VYELDVQAKD LGPNSIPAHC KVTVSVLDTN DNPPVINLLS VNSELVEVSE
   361  SAPPGYVIAL VRVSDRDSGL NGRVQCRLLG NVPFRLQEYE SFSTILVDGR LDREQHDQYN
   421  LTIQARDGGV PMLQSAKSFT VLITDENDNH PHFSKPYYQV IVQENNTPGA YLLSVSARDP
   481  DLGLNGSVSY QIVPSQVRDM PVFTYVSINP NSGDIYALRS FNHEQTKAFE FKVLAKDGGL
   541  PSLQSNATVR VIILDVNDNT PVITAPPLIN GTAEVYIPRN SGIGYLVTVV KAEDYDEGEN
   601  GRVTYDMTEG DRGFFEIDQV NGEVRTTRTF GESSKSSYEL IVVAHDHGKT SLSASALVLI
   661  YLSPALDAQE SMGSVNLSLI FIIALGSIAG ILFVTMIFVA IKCKRDNKEI RTYNCSNCLT
   721  ITCLLGCFIK GQNSKCLHCI SVSPISEEQD KKTEEKVSLR GKRIAEYSYG HQKKSSKKKK
   781  ISKNDIRLVP RDVEETDKMN VVSCSSLTSS LNYFDYHQQT LPLGCRRSES TFLNVENQNT
   841  RNTSANHIYH HSFNSQGPQQ PDLIINGVPL PETENYSFDS NYVNSRAHLI KSSSTFKDLE
   901  GNSLKDSGHE ESDQTDSEHD VQRSLYCDTA VNDVLNTSVT SMGSQMPDHD QNEGFHCREE
   961  CRILGHSDRC WMPRNPMPIR SKSPEHVRNI IALSIEATAA DVEAYDDCGP TKRTFATFGK
  1021  DVSDHPAEER PTLKGKRTVD VTICSPKVNS VIREAGNGCE AISPVTSPLH LKSSLPTKPS
  1081  VSYTIALAPP ARDLEQYVNN VNNGPTRPSE AEPRGADSEK VMHEVSPILK EGRNKESPGV
  1141  KRLKDIVL

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against PCDH19 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)
0.47
Highest tissue expression
6.4 nTPM

Expression across tissuesHPA

Tissue

  • cerebral cortex: 6.4 nTPM
  • hypothalamus: 4.8 nTPM
  • hippocampal formation: 3.8 nTPM
  • amygdala: 3.3 nTPM
  • adipose tissue: 1.7 nTPM
  • breast: 1.6 nTPM

Single-cell type

  • oligodendrocyte progenitor cells: 72 nCPM
  • retinal amacrine cells: 66 nCPM
  • brain excitatory neurons: 53 nCPM
  • other brain neurons: 53 nCPM
  • brain inhibitory neurons: 53 nCPM
  • vascular endothelial cells: 23 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

  • hypothalamus: 58 nTPM
  • hippocampal formation: 37 nTPM
  • cerebral cortex: 36 nTPM
  • basal ganglia: 29 nTPM
  • amygdala: 28 nTPM
  • pons: 23 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about PCDH19.

Disease | AllUniProt

Conditions PCDH19 is implicated in, by any mechanism.

  • Developmental and epileptic encephalopathy 9 (DEE9) MIM:300088

Disease | GeneticClinVar

442 pathogenic / likely-pathogenic of 1,566 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

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)
0.13
gnomAD pLI
1
gnomAD missense Z
2.59
DepMap mean gene effect
-0.05
DepMap dependency class
selective

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 1% 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 PCDH19 as an antibody target. Whether an autoantibody or antibody against PCDH19 could matter depends on whether native PCDH19 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

PCDH19 is annotated at the cell surface, where native PCDH19 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 PCDH19 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

Canonical record: https://seroatlas.com/gene/PCDH19. 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).

© 2026 · Seroatlas, Discover Oregon LLC · Terms of use

Loading the interactive Seroatlas protein explorer...