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Gene

PCDH19

protocadherin 19

Summary

Cytogenetic location
Xq22.1
Coordinates
Chromosome X: 100,291,644–100,410,273 (GRCh38)
Exons
6 exons across 118.6 kb
Protein
1,148 amino acids
Also known as
KIAA1313, EIEE9
Previous symbols
EFMR
MANE Select transcript
ENST00000373034.8NM_001184880.2
Locus type
gene with protein product
  • Very high
  • Confident
  • Low
  • Very low

Reference genomeGRCh38

Positions on gene and variant pages follow this choice, in this browser.

Curated reports relevant to this gene

  • Epilepsy (Full Panel)

    • X-Linked Complex Neurodevelopmental Disorder

      A complex neurodevelopmental disorder that is transmitted via X-linked inheritance, and is characterized by intellectual disability, autism and epilepsy.

      • ClinGen rates the link definitive
      • 4 GenCC submitters rate it definitive or strong
    • Epilepsy

      One of 171 genes linked to it

      A brain disorder characterized by episodes of abnormally increased neuronal discharge resulting in transient episodes of sensory or motor neurological dysfunction, or psychic dysfunction. These episodes may or may not be associated with loss of consciousness or convulsions.

      • 3 GenCC submitters rate it definitive or strong

Broader groupings

How PCDH19 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome X, with a bracket where PCDH19 sits. PCDH19 and 6 genes near it on chromosome X, from 99,850,959 to 100,850,958.Chromosome XXq22.1p22.33p22.32p22.31p22.2p22.13p22.12p22.11p21.3p21.2p21.1p11.4p11.3p11.23p11.22p11.21p11.1q11.1q11.2q12q13.1q13.2q13.3q21.1q21.2q21.31q21.32q21.33q22.1q22.2q22.3q23q24q25q26.1q26.2q26.3q27.1q27.2q27.3q28100 Mb100.2 Mb100.4 Mb100.6 Mb100.8 MbPCDH19: 100,291,644–100,410,273, reverse strandPCDH19TNMD: 100,584,929–100,601,108, forward strandTNMDTSPAN6: 100,627,080–100,639,991, reverse strandTSPAN6SRPX2: 100,644,195–100,675,788, forward strandSRPX2SYTL4: 100,671,783–100,732,154, reverse strandSYTL4CSTF2: 100,820,331–100,843,533, forward strandCSTF2NOX1: 100,843,324–100,874,464, reverse strandNOX1Diagram of PCDH19: 6 exons on the reverse strand of chromosome XExon 6: 8 known disease-causing sitesExon 5: 4 known disease-causing sitesExon 4: 7 known disease-causing sitesExon 3: 27 known disease-causing sitesExon 2: 2 known disease-causing sitesExon 1: 246 known disease-causing sitesExon 6: 100,291,644–100,296,875, 5,232 basesExon 5: 100,341,903–100,342,075, 173 basesExon 4: 100,350,646–100,350,704, 59 basesExon 3: 100,402,524–100,402,851, 328 basesExon 2: 100,403,524–100,403,664, 141 basesExon 1: 100,406,451–100,410,273, 3,823 bases64215′3′

Exons of the gene's MANE Select transcript (release v1.5), from NCBI and EMBL-EBI, on the GRCh38 reference genome.

Chromosome bands from UCSC's GRCh38 ideogram (2022-10-29).

Nearby genes from Ensembl release 116, on GRCh38.

Exons make up 9.8 kb of the gene's 118.6 kb; 3,447 of those bases code for the protein.

How a genome test reads PCDH19

302

positions in PCDH19 where ClinVar classes a change as pathogenic or likely pathogenic

None of them falls in a region short reads find hard.

A whole genome covers all 118.6 kb of PCDH19, introns included, not only the 9.8 kb of exons.

Where this comes from

  • HGNC: the gene's symbol, name, other symbols and location.
  • MANE Select v1.5, from NCBI and EMBL-EBI: the transcript, its exons and coding sequence.
  • GenCC and ClinGen, released 2026-10-16: which conditions the gene is linked to, and how strongly.
  • The ACMG secondary findings list, SF v3.2.
  • ClinVar and the GIAB stratifications: known disease-causing sites, and the regions short reads find hard.
  • The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
  • Data release 2026.10.16-c6eea6bf.

Cite this page

APA

Dante Labs. (n.d.). PCDH19 gene: protocadherin 19. Retrieved 17 October 2026, from https://dantelabs.com/genes/pcdh19

Vancouver

Dante Labs. PCDH19 gene: protocadherin 19 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/pcdh19

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