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Any early infantile epileptic encephalopathy in which the cause of the disease is a mutation in the CDKL5 gene.
Features include always present findings: EEG with generalized slow activity and Global developmental delay; and very common findings: Generalized tonic seizure. 71 total HPO annotations.
Organ System | Phenotype Count | Example Features |
|---|---|---|
Brain and nerves | 25 | Inability to walk, Generalized myoclonic seizure, Seizure |
Arms and legs | 5 | Short foot, Tapered finger, Small hand |
Muscles | 4 | Low muscle tone (hypotonia), Generalized hypotonia, Delayed gross motor development |
Digestive system | 4 | Gastroesophageal reflux, Constipation, Gastrostomy tube feeding in infancy |
Head and neck | 4 | Thick lower lip vermilion, Progressive microcephaly, Everted lower lip vermilion |
Bones and joints | 2 | Sideways curvature of the spine (scoliosis), Excessive outward curvature of the upper spine (kyphosis) |
Lungs and breathing | 2 | Apnea, Recurrent lower respiratory tract infections |
Eyes | 1 | Cerebral visual impairment |
Growth and development | 1 | Growth delay |
Blood and immune system | 1 | Recurrent lower respiratory tract infections |
CDKL5 deficiency disorder (CDD) is a developmental and epileptic encephalopathy (DEE) characterized by severe early-onset epilepsy and motor, cognitive, visual, and autonomic disturbances [, , , , , , , ]. Movement disorders include chorea, dystonia, and stereotypical hand and leg movements . Cardiac involvement is nonspecific . Because the full spectrum of phenotypic severity is still emerging, especially given the possibility of mosaicism (in males and females) and the potential for skewed X-chromosome inactivation (in females), an individual with a de novo CDKL5 pathogenic variant may have a mild phenotype (for example, minimal epilepsy and global developmental delays). To date, approximately 500 individuals have been identified with CDD .
Source: GeneReviews — "CDKL5 Deficiency Disorder"
CDKL5 encodes cyclin dependent kinase like 5 (960 aa). Mediates phosphorylation of MECP2. May regulate ciliogenesis Highest expression in Brain Frontal Cortex BA9 (11.9 TPM) and Artery Aorta (8.4 TPM).
Developmental and epileptic encephalopathy, 2 is associated with mutations in the CDKL5 gene on chromosome X.
The CDKL5 protein participates in Transcriptional Regulation by MECP2, Loss of function of MECP2 in Rett syndrome, and Regulation of MECP2 expression and activity pathways.
CDKL5 is classified as a druggable target (Druggable Genome, Enzyme, Kinase, Serine Threonine Kinase, and Tumor Suppressor categories) with score 2.9.
While genotype-phenotype correlations are emerging , there are two caveats regarding ascertainment: (1) the frequency of recurrent CDKL5 pathogenic variants is relatively low; and (2) measurements of severity with sufficient granularity to differentiate clinical severity have only recently become available. CDKL5 pathogenic variants causing CDD are typically loss-of-function variants ; however, duplications and missense gain-of-function variants associated with different, and often milder, neurologic manifestations have been reported. Phenotypes associated with nonsense alterations throughout the protein appear equally severe, suggesting that truncating variants located within the terminal region of the gene may be less severe .
Source: GeneReviews — "CDKL5 Deficiency Disorder"
For the purposes of this GeneReview, the terms "male" and "female" are narrowly defined as the individual's biological sex at birth as it determines clinical care . Diagnostic criteria for CDKL5 deficiency disorder (CDD) have been proposed .
CDD should be suspected in females and males with motor and cognitive developmental delays and epilepsy with onset in the first year of life (developmental delays and early-onset epilepsy constitute the minimal clinical diagnostic criteria proposed by ). Note: (1) Although females are more commonly affected than males with this X-linked disorder, the severity of manifestations in affected females and males can be equivalent.
Source: GeneReviews — "CDKL5 Deficiency Disorder"
Table 3. Developmental and Epileptic Encephalopathies in the Differential Diagnosis of CDKL5 Deficiency Disorder
Gene(s) | Disorder | MOI |
|---|---|---|
ARX | ARX-related DEE (OMIM 308350) | XL FOXG1 |
GABRA1 | GABRA1-related DEE (OMIM 615744) | AD |
GABRB3 | GABRB3-related DEE (OMIM 617113) |
Genetic testing for CDKL5 is available. Testing is considered confirmatory for diagnosis.
Biomarker and diagnostic research for developmental and epileptic encephalopathy, 2 has been reported in the published literature.
No approved treatments are currently available for developmental and epileptic encephalopathy, 2. The disease remains an area of unmet medical need.
International consensus recommendations for the assessment and management of individuals with CDKL5 deficiency disorder (CDD) have been published (full text). The management of individuals with CDD is complex and requires multiple specialty appointments; referral to a CDKL5 Center of Excellence may allow families to more easily coordinate care for affected individuals (to date, ten CDKL5 Centers of Excellence have been established in the United States).
To establish the extent of disease and needs in an individual diagnosed with CDD, the evaluations summarized (if not performed as part of the evaluation that led to the diagnosis) are recommended.
Table 4.
CDKL5 Deficiency Disorder: Recommended Evaluations Following Initial Diagnosis
System/Concern | Evaluation | Comment
| Measurement of OFC, length, weight | • Smaller OFC is assoc w/ severity of disorder.1
Poor weight gain can reflect nutritional status.
| Eval of epilepsy by neurologist or epileptologist | • EEG to assess EEG background, epileptiform activity, seizure type correlate w/clinical semiology
Prolonged video EEGs may be required to characterize spells of unclear etiology or rule out subclinical status epilepticus.
Eval of movement disorders | To characterize movement disorder, if present, ascertain effect on gross fine motor skills
Ophthalmologic/
| Ophthalmologist | Assess for visual acuity, abnormal ocular movement, refractive errors, strabismus
Source: GeneReviews — "CDKL5 Deficiency Disorder"
Several therapies have been investigated or are ongoing for CDD including the following:
Soticlestat/TAK935 (NCT03694275)
Ataluren (NCT02758626)
Fenfluramine (NCT03861871, NCT05064878)
Canabidiol
Ketogenic diet
Vagal nerve stimulation
Protein and gene replacement therapies have been proposed.
Clinical trials and registries assessing natural history and outcome measures are ongoing (NCT05558371, NCT05373719, NCT04486768). Search ClinicalTrials.gov in the US and EU Clinical Trials Register in Europe for access to information on clinical studies for a wide range of diseases and conditions.
Source: GeneReviews — "CDKL5 Deficiency Disorder"
4 trials found
To monitor existing manifestations, the individual's response to supportive care, and the emergence of new manifestations, the evaluations summarized in are recommended. In general, annual assessments by a medical home/primary care physician and specialists are needed.
Table 7.
CDKL5 Deficiency Disorder: Recommended Surveillance
System/Concern | Evaluation | Frequency
| Measurement of OFC, length, weight | Annually, or more frequently as required for mgmt
| Monitor those w/seizures as clinically indicated. | At each annual visit
Assess for new manifestations such as seizures, changes in tone, movement disorders. | At each visit
| • Measurement of growth parameters
Eval of nutritional status safety of oral intake
Eval of feeding time
| Monitor developmental progress educational needs.
Neurobehavioral/
| Assessment for sleep, anxiety, ADHD, ASD, aggression, self-injury
| Monitor for feeding, nutrition, constipation, GERD.
| Monitor for evidence of aspiration respiratory insufficiency.
| • Physical medicine, OT/PT assessment of mobility, self-help skills
Assessment of large joint mobility (e.g., hip surveillance)
Clinical eval of spine
Spine radiograph as needed to identify progressive scoliosis
Referral to orthopedist if Cobb angle 45 degrees for consideration of surgical correction
| At each annual visit
| Assess family need for social work support (e.g., palliative/respite care, home...
Source: GeneReviews — "CDKL5 Deficiency Disorder"
Phenotype severity distribution: 2 always present features, 1 very common feature, 41 common features.
Estimated prevalence: Unknown (Unknown prevalence).
4 clinical trials registered, 1 recruiting. Interventions under study include other interventions and drug therapy. Pipeline includes 1 PHASE3, 1 NA. Research is sponsored by a mix of industry and academic institutions.
98 publications have been identified in PubMed for developmental and epileptic encephalopathy, 2. Research spans Basic Science / Preclinical (40%), Review / Meta-Analysis (14%), and Epidemiology / Natural History (13%).
Research Type | Count | % of Total |
|---|---|---|
Laboratory research | 39 | 40% |
Research summaries | 14 | 14% |
Disease patterns and progression | 13 | 13% |
Patient case studies | 10 | 10% |
New treatment approaches | 9 | 9% |
Testing and diagnosis research | 7 | 7% |
Other research | 3 | 3% |
Clinical study results | 3 | 3% |
Loi M (2026). [PMID: 41898635](https://pubmed.ncbi.nlm.nih.gov/41898635/). *Int J Mol Sci*. [Basic Science / Preclinical]
Arshad MN (2026). [PMID: 41709000](https://pubmed.ncbi.nlm.nih.gov/41709000/). *Exp Mol Med*. [Basic Science / Preclinical]
Basu S (2026). [PMID: 41266835](https://pubmed.ncbi.nlm.nih.gov/41266835/). *Indian J Pediatr*. [Other]
Coletti A (2026). [PMID: 42188286](https://pubmed.ncbi.nlm.nih.gov/42188286/). *Mar Drugs*. [Gene Therapy / Novel Therapeutics]
Chai Y (2026). [PMID: 41963441](https://pubmed.ncbi.nlm.nih.gov/41963441/). *Sci Rep*. [Gene Therapy / Novel Therapeutics]
Liogier d'Ardhuy X (2026). [PMID: 41531035](https://pubmed.ncbi.nlm.nih.gov/41531035/). *Epilepsia*. [Epidemiology / Natural History]
Emery BA (2026). [PMID: 42246027](https://pubmed.ncbi.nlm.nih.gov/42246027/). *Front Neurosci*. [Basic Science / Preclinical]
Boggio Bozzo S (2026). [PMID: 41807047](https://pubmed.ncbi.nlm.nih.gov/41807047/). *Life Sci Alliance*. [Basic Science / Preclinical]
Zubiete-Franco I (2026). [PMID: 42167577](https://pubmed.ncbi.nlm.nih.gov/42167577/). *J Biol Chem*. [Gene Therapy / Novel Therapeutics]
Katayama S (2026). [PMID: 41967861](https://pubmed.ncbi.nlm.nih.gov/41967861/). *J Biochem*. [Basic Science / Preclinical]
Data assembled from 8 of 12 sources · Last updated Sep 19, 2026, 6:54 PM UTC
Online Mendelian Inheritance in Man
European rare disease database
Genetic and Rare Diseases Info Center
GABRG2 | GABRG2-related DEE (OMIM 618396) | AD GRIN2A |
KCNQ2 | KCNQ2-related developmental epileptic encephalopathy (OMIM 613720) | AD KCNT1 |
MECP2 | MECP2 classic Rett syndrome (See MECP2 Disorders.) | XL MECP2 duplication syndrome |
PCDH19 | PCDH19-related DEE (OMIM 300088) | XL SCN1A |
SCN2A | SCN2A-related DEE (OMIM 613721) | AD SCN8A |
SLC2A1 | Classic glucose transporter type 1 deficiency syndrome (See Glucose Transporter Type 1 Deficiency Syndrome.) | AD(AR)1 STXBP1 |
Source: GeneReviews — "CDKL5 Deficiency Disorder"