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Gene

CDKL5

cyclin dependent kinase like 5

Summary

Cytogenetic location
Xp22.13
Coordinates
Chromosome X: 18,425,608–18,640,196 (GRCh38)
Exons
18 exons across 214.6 kb
Protein
960 amino acids
Inheritance
X-linked dominant
Also known as
EIEE2, CFAP247
Previous symbols
STK9
MANE Select transcript
ENST00000623535.2NM_001323289.2
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 report relevant to this gene

  • Epilepsy (Full Panel)

    • CDKL5 Deficiency DisorderX-linked dominant

      A developmental and epileptic encephalopathy caused by CDKL5 variants, with seizures beginning in the first months of life and severe developmental delay.

      • ClinGen rates the link definitive
      • 4 GenCC submitters rate it definitive or strong
      What knowing changes

      Ganaxolone is FDA-approved for seizures associated with CDKL5 deficiency disorder.

    • Atypical Rett Syndrome

      A neurodevelopmental disorder that is diagnosed when a child presents with a Rett-like syndrome but does not fulfill all the diagnostic criteria for typical Rett syndrome (classic/typical RTT).

      • 3 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

Inheritance

X-linked dominant
The change is on the X chromosome, and one copy is enough. A mother who has it passes it on to each child with a one-in-two chance; a father, to all of his daughters and none of his sons.

How CDKL5 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
  • Variants with a page
Chromosome X, with a bracket where CDKL5 sits. CDKL5 and 6 genes near it on chromosome X, from 18,032,902 to 19,032,901.Chromosome XXp22.13p22.33p22.32p22.31p22.2p22.13p22.12p22.11p21.3p21.2p21.1p11.4p11.3p11.23p11.22p11.21p11.1q11.1q11.2q12q13.1q13.2q13.3q21.1q21.2q21.31q21.32q21.33q22.1q22.2q22.3q23q24q25q26.1q26.2q26.3q27.1q27.2q27.3q2818.2 Mb18.4 Mb18.6 Mb18.8 Mb19 MbBEND2: 18,162,931–18,220,886, reverse strandBEND2SCML2: 18,239,307–18,355,149, reverse strandSCML2CDKL5: 18,425,608–18,640,196, forward strandCDKL5RS1: 18,639,688–18,672,108, reverse strandRS1PPEF1: 18,675,909–18,828,342, forward strandPPEF1PHKA2: 18,889,806–18,984,998, reverse strandPHKA2ADGRG2: 18,989,307–19,122,962, reverse strandADGRG2Diagram of CDKL5: 18 exons on the forward strand of chromosome XExon 2: 10 known disease-causing sitesExon 3: 6 known disease-causing sitesExon 4: 8 known disease-causing sitesExon 5: 24 known disease-causing sitesExon 6: 18 known disease-causing sitesExon 7: 15 known disease-causing sitesExon 8: 26 known disease-causing sitesExon 9: 32 known disease-causing sitesExon 10: 8 known disease-causing sitesExon 11: 22 known disease-causing sitesExon 12: 89 known disease-causing sitesExon 13: 8 known disease-causing sitesExon 14: 7 known disease-causing sitesExon 15: 9 known disease-causing sitesExon 16: 12 known disease-causing sitesExon 17: 12 known disease-causing sitesExon 18: 25 known disease-causing sitesExon 1: 18,425,608–18,425,695, 88 basesExon 2: 18,506,935–18,507,160, 226 bases. 2 variants with a page in exon 2. List themExon 3: 18,510,820–18,510,854, 35 bases. 3 variants with a page in exon 3. List themExon 4: 18,564,477–18,564,522, 46 bases. 1 variant with a page in exon 4. List themExon 5: 18,575,354–18,575,490, 137 bases. 3 variants with a page in exon 5. List themExon 6: 18,579,848–18,579,968, 121 bases. 3 variants with a page in exon 6. List themExon 7: 18,581,891–18,581,950, 60 bases. 1 variant with a page in exon 7. List themExon 8: 18,584,263–18,584,353, 91 bases. 5 variants with a page in exon 8. List themExon 9: 18,587,954–18,588,143, 190 bases. 4 variants with a page in exon 9. List themExon 10: 18,595,348–18,595,428, 81 basesExon 11: 18,598,462–18,598,613, 152 bases. 1 variant with a page in exon 11. List themExon 12: 18,603,902–18,604,868, 967 bases. 3 variants with a page in exon 12. List themExon 13: 18,608,811–18,608,912, 102 basesExon 14: 18,609,465–18,609,570, 106 bases. 2 variants with a page in exon 14. List themExon 15: 18,613,152–18,613,275, 124 basesExon 16: 18,619,867–18,619,966, 100 basesExon 17: 18,625,128–18,625,247, 120 basesExon 18: 18,628,371–18,640,196, 11,826 bases. 4 variants with a page in exon 18. List them1246810121416185′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 14.6 kb of the gene's 214.6 kb; 2,883 of those bases code for the protein.

How a genome test reads CDKL5

397

positions in CDKL5 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 214.6 kb of CDKL5, introns included, not only the 14.6 kb of exons.

Variants with a page (33)

The CDKL5 variants with a page here, most review stars first. Each page describes ClinVar's public record of the variant, never a result.

VariantHGVS c.Exon or intronPosition (GRCh38)ClinVar classificationReview status
A40Vc.119C>TExon 418,564,496Pathogenic3 stars out of 4 reviewed by expert panel
A157Pc.469G>CExon 818,584,268Likely pathogenic3 stars out of 4 reviewed by expert panel
A157Vc.470C>TExon 818,584,269Likely pathogenic3 stars out of 4 reviewed by expert panel
c.146-1G>AIntron 418,575,353Pathogenic3 stars out of 4 reviewed by expert panel
c.2151A>GExon 1418,609,569Likely pathogenic3 stars out of 4 reviewed by expert panel
C30Yc.89G>AExon 318,510,844Likely pathogenic3 stars out of 4 reviewed by expert panel
C152Rc.454T>CExon 718,581,941Likely pathogenic3 stars out of 4 reviewed by expert panel
D193Gc.578A>GExon 918,587,977Likely pathogenic3 stars out of 4 reviewed by expert panel
D193Vc.578A>TExon 918,587,977Likely pathogenic3 stars out of 4 reviewed by expert panel
E74Xc.220G>TExon 518,575,428Pathogenic3 stars out of 4 reviewed by expert panel

See all 33 CDKL5 variants →

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.). CDKL5 gene: cyclin dependent kinase like 5. Retrieved 17 October 2026, from https://dantelabs.com/genes/cdkl5

Vancouver

Dante Labs. CDKL5 gene: cyclin dependent kinase like 5 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/cdkl5

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