Clinical manifestations

Presentation and course

Epilepsy. The electroclinical course typically evolves over three successive stages (01).

Stage 1. Initially, children have frequent, brief, tonic seizures.

The median age of seizure onset is 6 weeks, with onset by 12 months in 90% of cases (11; 23). The interictal EEG may be normal at onset. Some of these children may reach seizure control after several months. Regardless of the ultimate epilepsy course, all patients at this stage already express hypotonia, sleepiness, and poor eye contact (11).

Stage 2. This stage is characterized by developmental stagnation and the appearance of epileptic spasms with or without hypsarrhythmia on EEG.

Stage 3. Seizures remain refractory and include tonic, myoclonic, and spasms occurring daily or multiple times per day in almost three quarters of patients (71%) (11). Most of them (73%) require a combination of more than two antiseizure medications. By this point, the interictal EEG remains abnormal, with high-amplitude slow waves and bursts of spikes and poly spikes.

A distinctive seizure type often seen during the course of this epileptic encephalopathy is the hypermotor-tonic-spasms sequence, and recognition of this specific sequential seizure may help the clinician in considering the diagnosis of a CDKL5 deficiency disorder (15).

Similar patterns of motor seizures with multiple sequences were identified in other case series, including tonic-vibratory-spasms-myoclonic seizures or focal tonic-clonic followed by spasms (24; 25).

Some patients may experience a “honeymoon period” with temporary seizure freedom. This may occur around 2 years of age (range: 2 months–11 years) and has a median duration of 6 months (range: 2.5 months–6 years) (11). This phase may indicate a potentially less severe epilepsy outcome but does not necessarily impact the severity of developmental impairment.

Development. Some degree of impairment is seen in all patients. Gross motor, fine motor, and speech-language development are impaired in all individuals with CDKL5 deficiency disorder. Hypotonia is a nearly universal feature (11). By the age of 5, nearly three quarters of girls achieve independent sitting, and almost one quarter (22%) achieve independent walking (09). However, only a quarter of boys achieve unaided sitting by the age of 1 year and 3 months.

Half of the affected girls can perform a raking grasp by the age of 5 years, and only 10% achieve pincer grip at any time, whereas only 10% of the affected boys achieve the raking grasp.

Less than half of children can babble by the age of 6, and only one quarter can speak single words by the age of 7 (09). The most common communication methods are body language, facial expressions, and simple sounds and gestures (08).

Associated features. Autistic features are prominent in CDKL5 deficiency disorder, often encompassing challenges with social interaction, communication difficulties, and repetitive behaviors. However, the formal diagnosis of autism spectrum disorder in the context of CDKL5 deficiency disorder can be particularly challenging due to the overlapping symptoms of developmental delay and severe epilepsy. Generally, males are more severely affected than females, although some males may present with a milder phenotype (28).

Another prominent feature of CDKL5 deficiency disorder is cortical visual impairment, defined as a visual dysfunction in the absence of ocular or anterior visual pathway abnormalities; it is present in more than three quarters of patients (31; 06). It manifests as poor eye fixation and gaze avoidance, along with abnormal eye movements, including esotropia, exotropia, and horizontal and rotatory nystagmus.

Arrest in head growth occurs in most patients (60%); however, only a minority (10%) would be classified as having acquired microcephaly (10; 28). Various unspecific dysmorphic features have also been described in individuals with a CDKL5 pathogenic variant, including large deep-set eyes, strabismus, high forehead, full lips, wide mouth, and widely spaced teeth (10).

Hand stereotypies were reported in 80% of children, less frequently in males. They are more consistent with self-stimulatory behavior (eg, putting hand in the mouth) versus the type of hand stereotypies observed in Rett syndrome. Stereotypical leg crossing is also common (28).

Approximately one third of patients have associated movement disorders, such as chorea and dystonia (17).

Most patients (87%) experience sleep disturbances, such as difficulty maintaining nighttime sleep and excessive daytime sleepiness.

Breathing abnormalities affect nearly one third (32.5%) of patients. Common issues include hyperventilation (13.6%) and breath holding (26.4%). Older individuals are more likely to experience autonomic-type breathing irregularities, with males being particularly susceptible to breath holding (23).

CDKL5 deficiency disorder also affects cardiac and gastrointestinal function. Gastrointestinal problems, including constipation, reflux, and air swallowing, are reported in 87% of patients. Feeding difficulties are another concern, with more than a quarter of patients experiencing issues and almost one third requiring gastrostomy feeding (23). Cardiac abnormalities, such as prolonged QT interval and structural changes, have been also observed (21).

Prognosis and complications

Prognosis. The prognosis for individuals with CDKL5 deficiency disorder is generally poor, with most patients experiencing refractory epilepsy and severe intellectual disability and requiring lifelong care. Only a minority achieve independent walking.

Over 80% of patients with CDKL5 deficiency disorder continue to experience frequent seizures despite multiple antiseizure medications.

The developmental outcome is influenced by several factors, including genetic variations, seizure management, and the presence of associated comorbidities.

Certain features may help predict or influence prognosis. Boys typically exhibit poorer gross motor function, fine motor skills, and communication abilities compared to girls. Cerebral visual impairment is most clearly associated with the achievement of developmental milestones (06). Cerebral visual impairment can be assessed in infancy and may serve as a valuable marker for severity, prognosis, or the need for more intensive therapies (27). Better early seizure control is associated with improved developmental trajectories, even after adjusting for genotype. This indicates that although genetic factors play a significant role, effective management of epilepsy may positively influence developmental outcomes (18).

Complications. CDKL5 deficiency disorder shares the complications of other developmental and epileptic encephalopathies, which are common across these severe conditions and not specific to the CDKL5 genetic defect. One of the most common complications is represented by respiratory infections. These can range from mild upper respiratory tract infections to severe pneumonia. They are common in the first 5 years of life and tend to decrease in frequency with age. This decrease may be associated in part with the insertion of a G-tube, which reduces the risk of infections caused by aspiration (23).

Orthopedic complications like scoliosis occur in the context of hypotonia in almost three quarters of patients (68.5%) (23).

The high seizure frequency and severity in patients with CDKL5 deficiency disorder are associated with a high risk of SUDEP, especially due to the daily and often nocturnal tonic or tonic-clonic seizures (28).

Biological basis

Etiology and pathogenesis

CDKL5 deficiency disorder is primarily caused by pathogenic variants in the CDKL5 gene. CDKL5 (cyclin-dependent kinase-like 5), also known as serine/threonine kinase 9 (STK9), is found at position 22 on the short arm of the X chromosome (Xp22).

Protein structure and function. CDKL5 comprises multiple exons, with the primary brain isoform being hCDKL5_1. The CDKL5 protein includes an N-terminal catalytic domain starting from exon 2, essential for its kinase activity, and a long C-terminal domain that may play regulatory roles.

Cellular localization and function. CDKL5 is highly expressed in the brain, particularly in the cerebral cortex, hippocampus, cerebellum, striatum, and brainstem. It is found in both the nucleus and cytoplasm of neurons, with a significant presence in dendrites and nuclear speckles involved in pre-mRNA splicing. The protein has a role in regulating axonal outgrowth, dendritic morphogenesis, and synapse formation in early postnatal life, and in maintaining synaptic function in the adult brain (38).

CDKL5 levels increase postnatally and stabilize at peak levels in the adult brain (30; 04; 29). In cortical neurons, CDKL5 knockdown leads to reduced dendritic and axonal length and delays in neuronal migration.

Molecular interactions. CDKL5 phosphorylates various substrates, including MECP2, DNMT1, and other proteins involved in neuronal function and synaptic stability. The interaction with MECP2, the protein implicated in Rett syndrome, suggests overlapping pathways between these disorders.

CDKL5 is involved in excitatory synapse stability, influencing the number and function of synaptic vesicles and the composition of synaptic proteins like PSD-95. Loss of CDKL5 results in a reduction of excitatory synapses and alterations in AMPA and NMDA receptor levels (26; 37).

Genetics. CDKL5 is a large protein of 1030 amino acids containing a conserved catalytic domain (amino acids 13–297, portion of protein responsible for kinase activity) within its N-terminus region where pathogenic missense variants are exclusively clustered. However, pathogenic variants that are outside the catalytic domain may also impart the protein function. Due to small cohorts and lack of recurrent pathogenic variants, the genotype-phenotype correlation has been challenging in CDKL5 deficiency disorder. However, it conducted to the classification of variants in four groups (09).

Type A. Absence of any functional protein, such as variants resulting in LOF components in the catalytic domain before amino acid 172 and all full gene deletions.

Type B. Missense variants in the catalytic domain, including any missense variants within the protein kinase active region or in frame mutations.

Type C. Truncating variants between aa 172 and 781, including nonsense or frameshift mutations resulting in maintaining kinase activity but loss of C-terminal region.

Type D. Truncating variants between aa 781 and 905 maintaining kinase activity and majority of the C-terminal region.

Patients with the type D variant group were found to perform better in gross motor, fine motor, and communication skills compared to other variant groups; the lowest seizure rate was found in the type C variant group (08; 11).

Mosaicism appears to play a protective role in males, and it could explain why some males achieve motor milestones similar to those of females (06).

Certain variants are associated with more severe phenotypes. For example, variants such as Arg178Trp and Arg559* are linked to higher clinical severity and lower developmental scores. In contrast, variants like Arg134* and Arg550* are associated with milder phenotypes, both in terms of clinical severity and developmental outcomes. Seizures can also be occasionally absent, especially in patients harboring pathogenic variants associated with a less pronounced reduction of kinase activity, such as the Ser215Arg variant (22).

Epidemiology

CDKL5 deficiency disorder is an ultra-rare condition, with an estimated incidence of 2.36 per 100,000 live births (95% CI: 0.805–5.59). This estimate is based on the identification of four cases over 3 years among 333 Scottish children with epilepsy onset before 36 months of age who underwent epilepsy gene panel testing (33).

Prevention

Genetic counseling. CDKL5 deficiency disorder is an X-linked disorder. Most probands represent isolated cases. Typically, the disorder is caused by a de novo germline and, more rarely, by postzygotic, pathogenic variants in the CDKL5 gene. Rarely, a patient with CDKL5 deficiency disorder has the disorder as a result of a pathogenic CDKL5 variant inherited from a mosaic asymptomatic mother. Girls who inherit the pathogenic variant are at high risk of being affected, although the pattern of X-chromosome inactivation and possibly of other environmental factors may result in a variable phenotype. Boys who inherit the pathogenic variant will be hemizygous and either do not survive fetal life or are severely affected. Once the pathogenic variant has been identified in an affected family member, families have the opportunity to address future reproductive choices and consider preimplantation genetic testing for subsequent pregnancies.

Differential diagnosis

Confusing conditions

Several other neurodevelopmental and neurogenetic disorders share overlapping features with CDKL5 deficiency disorder, making differential diagnosis challenging. Accurate diagnosis is essential for appropriate management and genetic counseling. The following are some initial diagnoses in patients with CDKL5 deficiency disorder.

Rett syndrome. Rett syndrome, particularly the early-onset variant, represents a frequent misdiagnosis. Both disorders primarily affect females and present with severe neurodevelopmental delay, early-onset seizures, and hypotonia. The following are key distinguishing features.

Genetic basis. Rett syndrome is caused by mutations in the MECP2 gene, whereas CDKL5 deficiency disorder is caused by mutations in the CDKL5 gene.

Clinical features. Although both conditions present with hand stereotypies and breathing irregularities, Rett syndrome is characterized by a period of normal development followed by regression, loss of purposeful hand skills (such as hand wringing), and more pronounced microcephaly compared to CDKL5 deficiency disorder (14). Additionally, CDKL5 deficiency disorder has a higher incidence of early-onset, treatment-resistant seizures.

EEG patterns. Rett syndrome has a characteristic four-stage progression in EEG abnormalities, whereas CDKL5 deficiency disorder shows progressively abnormal interictal EEGs without such staged progression.

Several channelopathies share clinical features with CDKL5 deficiency disorder at onset, during the early stages. For instance, KCNQ2 and SCN2A developmental and epileptic encephalopathy both present with neonatal-onset focal tonic seizures and developmental delay. KCNQ2-/SCN2A developmental and epileptic encephalopathy is often associated with more severe EEG abnormalities at onset, including burst suppression patterns not typically seen in CDKL5 deficiency disorder. In addition, the age at onset is typically in the very first days of life. Diagnosis is confirmed through genetic testing.

Infantile epileptic spasms syndrome, or West syndrome. The presence of epileptic spasms and developmental regression during stage 2 of CDKL5 deficiency disorder may lead to a more general diagnosis of infantile epileptic spasms. Some features may help in identifying CDKL5 deficiency disorder as a specific etiology, including the absence of hypsarrhythmia. A highly disorganized and chaotic EEG pattern is typically seen in West syndrome, whereas CDKL5 deficiency disorder often presents without hypsarrhythmia, even in the presence of epileptic spasms.

Diagnostic workup

Currently, the formal criteria for diagnosing CDKL5 deficiency disorder include the presence of early-onset seizures, typically within the first 3 months of life, significant neurodevelopmental delay, and pathogenic variants in the CDKL5 gene identified through genetic testing (02).

EEG. The interictal EEG is usually normal during the initial stage. However, as the condition progresses to the second stage, the EEG shows bilateral or generalized slowing along with spikes or polyspikes. During the second stage, hypsarrhythmia may be present in less than a half (47%) of patients with epileptic spasms (06). In the third stage, this is followed by high-amplitude diffuse delta waves with pseudoperiodic bursts of high-amplitude spikes, polyspikes, and spikes and waves (01). Buoni and colleagues studied the electroclinical pattern of epilepsy in three patients with CDKL5 deficiency disorder (03). They emphasized a specific epileptic pattern that consisted of myoclonic epilepsy with refractory seizures, corresponding to the third stage, and a “unique EEG pattern” that included diffuse and high-amplitude continuous sharp waves with multifocal spikes and interictal pseudoperiodic diffuse polyspike or wave discharges.

Neuroimaging. The MRI may be normal, or nonspecific brain abnormalities may be present in males more than in females, including progressive cortical and cerebellar atrophy with reduction of grey and white matter thickness (32). MRI helps differentiate CDKL5 deficiency disorder from other conditions like structural malformations, metabolic disorders, or other genetic syndromes with characteristic imaging findings.

Genetic analysis. The diagnosis is confirmed by the presence of a pathogenic or likely pathogenic CDKL5 variant in a heterozygous state in a female, or a hemizygous state in a male, identified by molecular genetic testing. Pathogenic variants identified by next-generation sequencing can include missense mutations, nonsense mutations, small insertions/deletions, and larger genomic deletions or duplications. Multiplex ligation-dependent probe amplification can be used to detect larger deletions or duplications that may not be identified by sequencing alone (24).

Identifying CDKL5 deficiency disorder at presentation in the first weeks of life can be challenging, and most patients are often diagnosed later in life. However, the onset of brief tonic-spasm seizures in a girl with normal interictal EEG should prompt consideration of CDKL5 pathogenic variants.

Management

Seizure management. Pharmacological management in CDKL5 deficiency disorder aims to reduce seizure frequency and improve overall quality of life, though achieving complete seizure freedom is rarely possible.

To date, no specific antiseizure medications have been shown to have greater efficacy for seizure control in this particular epileptic encephalopathy. Commonly used antiseizure medications, including carbamazepine, valproate, and clobazam, have been trialed in order to control the tonic seizures, with different results. In addition, the medications chosen during the clinical course that includes infantile spasms is no different than other idiopathic or cryptogenic spasms, with most clinicians using ACTH or another steroid derivative, and vigabatrin.

Ganaxolone, a neuroactive steroid, has emerged as a potential treatment for CDKL5 deficiency disorder–associated refractory epilepsy. A phase 3 trial of patients aged 2 to 21 years showed a 30% reduction in seizure frequency in patients treated with ganaxolone and a 6.9% reduction in patients receiving placebo (16).

Fenfluramine has shown effectiveness in reducing seizure frequency, particularly tonic-clonic seizures, in patients with CDKL5 deficiency disorder. Recent trials have provided encouraging results, with a notable (50% to 90%) reduction in seizure frequency (07).

Studies indicate that cannabidiol can be beneficial in managing seizures in CDKL5 deficiency disorder (05). The ketogenic diet has also shown some efficacy in reducing seizure frequency. A study involving over 100 patients with CDKL5 deficiency disorder reported that two thirds of those on ketogenic diet experienced improvements in seizure activity, although long-term efficacy remains a challenge due to side effects and dietary adherence issues (20).

Vagal nerve stimulation is considered for patients with refractory epilepsy who do not respond adequately to any antiseizure medications. Vagal nerve stimulation can help reduce seizure frequency and improve quality of life, although its efficacy in CDKL5 deficiency disorder needs further validation (19).

Multidisciplinary care. Multidisciplinary care is crucial for managing CDKL5 deficiency disorder, addressing not only seizures but also comorbidities, such as intellectual disability, motor dysfunction, and gastrointestinal issues. A multidisciplinary team typically includes neurologists, dietitians, physiotherapists, and gastroenterologists to provide comprehensive care tailored to each patient's needs. Management of comorbidities includes the following.

Gastrointestinal and feeding issues. Patients with gastrointestinal issues may require specific dietary interventions or feeding tubes. Coordination with dietitians is essential.

Developmental support. Physical, occupational, and speech therapy are integral parts of the management plan to support motor and cognitive development.

Behavioral and sleep issues. Addressing sleep disturbances and behavioral problems through appropriate medications, such as melatonin, and behavioral therapies is important for improving overall quality of life.

Treatments on the horizon. Research into gene therapy offers hope for disease-modifying treatments in CDKL5 deficiency disorder. Additionally, novel pharmacological agents targeting specific molecular pathways involved in CDKL5 deficiency are under investigation and may provide new therapeutic options in the future. Recent advancements include gene therapy approaches, such as adeno-associated virus (AAV)-mediated CDKL5 gene replacement, which have shown promising results in preclinical models by improving motor functions and correcting cellular defects (12). Other potential therapies involve protein substitution and RNA-based therapeutics aimed at restoring CDKL5 function (35). These innovative treatments offer hope for significantly enhancing the quality of life for children affected by CDKL5 deficiency disorder.

Outcomes

The seizure outcome is generally poor due to the refractory nature of seizures and the heterogeneity of clinical manifestations. Although some patients experience some reductions in seizure frequency, achieving complete seizure freedom is rare. The focus of treatment, therefore, often shifts to improving the quality of life and managing comorbidities.

Complications from treatment are common due to the polypharmacy often required to manage CDKL5 deficiency disorder. Side effects from antiseizure medications include the following.

Sedation and cognitive impairment. This is common with many antiseizure medications, particularly benzodiazepines like clobazam.

Gastrointestinal issues. These are often seen with valproic acid and dietary therapies like the ketogenic diet.

Behavioral changes. Some antiseizure medications and dietary treatments can lead to increased irritability and behavioral issues.

Reported side effects in patients treated with ganaxolone include somnolence, dizziness, and fatigue, although these were generally manageable and did not lead to significant treatment discontinuation.

Cannabidiol side effects, such as gastrointestinal disturbances, altered liver enzymes, and interactions with other antiseizure medications, are common and require regular monitoring.