Kisho is an information platform, not a medical provider. Nothing on this site constitutes medical advice, diagnosis, or treatment recommendations. All content is aggregated from publicly available sources (including ClinicalTrials.gov, PubMed, FDA.gov, and Orphanet) and is provided for informational purposes only. Clinical trial eligibility, treatment decisions, and any health-related actions should always be discussed with a qualified healthcare professional. Kisho does not endorse any specific therapy, organization, or clinical trial. Terms of use · Privacy policy
Features include always present findings: Dystonia, Focal impaired awareness seizure, Low muscle tone (hypotonia), and Microcephaly and others; and sometimes findings: Strabismus, Sideways curvature of the spine (scoliosis), and Atypical behavior. 30 total HPO annotations.
Organ System | Phenotype Count | Example Features |
|---|---|---|
Brain and nerves | 19 | Mild intellectual disability, Dystonia, Seizure |
Muscles | 4 | Cerebral cortical atrophy, Low muscle tone (hypotonia), Generalized hypotonia |
Head and neck | 4 | Coarse facial features, Microcephaly, Long face |
Eyes | 2 | Strabismus, Cerebral visual impairment |
Arms and legs | 1 | Lower limb spasticity |
Bones and joints | 1 | Sideways curvature of the spine (scoliosis) |
CLCN4-related neurodevelopmental disorder (CLCN4-NDD), an X-linked disorder, is characterized in the 36 males reported to date by developmental delay or intellectual disability, behavioral/mental health issues (e.g., autism spectrum disorder, anxiety, hyperactivity, and bipolar disorder), epilepsy, and gastrointestinal dysfunction. The five heterozygous females with a de novo CLCN4 variant reported to date had findings very similar to those of affected males. Twenty-two of 25 heterozygous females identified in family studies following identification of an affected male were unaffected or had only mild specific learning difficulties and/or mental health concerns; three were more severely affected. The findings of affected individuals reported to date are summarized in . Table 2. Features in Affected Males and Heterozygous Females with CLCN4 Variants
Feature | HemizygousMales (n=36) | Heterozygous Females |
|---|---|---|
function | Borderline ID | 1/36 |
Mild ID | 9/36 | 0/5 |
Moderate ID | 9/36 | 2/5 |
Severe/profound ID | 17/36 | 2/5 |
Normal cognitive function | 0 | 0 |
medication | Epilepsy | 22/36 |
Well controlled | 8/22 | 1/2 |
Drug resistant | 12/22 | 1/2 |
Data re seizure control NA | 2/22 | — |
Other | Behavioral issues/ Mentalhealth disorders | 23/36 |
Infantile hypotonia | 11/36 | 3/5 |
Progressive neurologicmanifestations | 8/36 | 1/5 |
Abnormal MRI findings | 14/18 tested | 2/4 tested |
Significant GI involvement | 3/36 | 2/5 |
Scoliosis | 3/36 | 1/5 |
Source: GeneReviews — "CLCN4-Related Neurodevelopmental Disorder"
CLCN4 encodes Cl-/H+ antiporter 4 (760 aa). Strongly outwardly rectifying, electrogenic H(+)/Cl(-)exchanger which mediates the exchange of chloride ions against protons. Highest expression in Brain Cerebellar Hemisphere (54.4 TPM) and Brain Cerebellum (41.5 TPM).
Intellectual disability, X-linked 49 is associated with mutations in the CLCN4 gene on chromosome X.
The CLCN4 protein participates in CLCN4/5/6 exchange Cl- for H+ pathway.
CLCN4 is classified as a druggable target (Druggable Genome, Ion Channel, and Transporter categories) with score 2.2.
No genotype-phenotype correlations have been identified to date. Significant phenotypic variability has been observed both between individuals from different families with a recurrent variant and among individuals from a single family who have the same variant . The phenotypes of males with haploinsufficiency (due to exon deletions or frameshift or nonsense variants) were noted to be relatively milder than the phenotypes of individuals with missense variants .
Source: GeneReviews — "CLCN4-Related Neurodevelopmental Disorder"
No consensus clinical diagnostic criteria for CLCN4-related neurodevelopmental disorder have been published.
CLCN4-related neurodevelopmental disorder (CLCN4-NDD) should be considered in individuals with the following clinical and brain MRI findings and family history.
Clinical findings
Developmental delay or intellectual disability
Autism spectrum disorder
Epilepsy
Mental health conditions including anxiety and bipolar disorder
Gastrointestinal dysfunction
Unremarkable facial features. Although a subtle lengthening of the face and squaring of the chin that becomes more prominent with age has been noted in several individuals (see Figure 3 in ; full text), these features are not likely to be distinctive enough to trigger consideration of this specific diagnosis.
Source: GeneReviews — "CLCN4-Related Neurodevelopmental Disorder"
Because the phenotypic features associated with CLCN4-related neurodevelopmental disorder are not sufficient to diagnose this condition, all disorders with intellectual disability, autism spectrum disorder, and epilepsy without other distinctive findings should be considered in the differential diagnosis. See OMIM Phenotypic Series:
• Autosomal Dominant Intellectual Developmental Disorder
• Autosomal Recessive Intellectual Developmental Disorder
• Nonsyndromic X-Linked Intellectual Developmental Disorder
• Syndromic X-Linked Intellectual Developmental Disorder
• Developmental and Epileptic Encephalopathy
• Idiopathic Generalized Epilepsy
• Susceptibility to Autism
Source: GeneReviews — "CLCN4-Related Neurodevelopmental Disorder"
Genetic testing for CLCN4 is available. Testing is considered confirmatory for diagnosis.
Biomarker and diagnostic research for intellectual disability, X-linked 49 has been reported in the published literature.
No approved treatments are currently available for intellectual disability, X-linked 49. The disease remains an area of unmet medical need.
No consensus clinical practice guidelines for CLCN4-related neurodevelopmental disorder have been published; the following management recommendations are based on review of the literature [, , , , , , ] and the authors' personal observations. Evaluations Following Initial Diagnosis To establish the extent of disease and needs in an individual diagnosed with CLCN4-related neurodevelopmental disorder (CLCN4-NDD), the evaluations summarized (if not performed as part of the evaluation that led to the diagnosis) are recommended. Table 3. Recommended Evaluations Following Initial Diagnosis in Individuals with CLCN4-Related Neurodevelopmental Disorder
System/Concern | Evaluation | Comment |
|---|---|---|
Constitutional | Measure height,weight, headcircumference. | — |
Development | Developmentalassessment | To incl motor, adaptive, cognitive, speech/language eval; Eval for early intervention/ educational support |
Neurologic | Neurologic eval | Eval for epilepsy, hypotonia, spasticity, abnormal mvmts/ ataxia; Consider EEG if seizures are a concern.; Consider brain MRI as part of investigation for neurologic manifestations (e.g., therapy-resistant epilepsy). Psychiatric/ |
Behavioral | Neuropsychiatriceval | For persons age 12 mos: screen for behavior concerns incl sleep disturbances, ADHD, anxiety, bipolar disorder, /or traits suggestive of ASD. Musculoskeletal/ |
ADL |
Source: GeneReviews — "CLCN4-Related Neurodevelopmental Disorder"
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. Note: There may not be clinical trials for this disorder.
Source: GeneReviews — "CLCN4-Related Neurodevelopmental Disorder"
View trials for intellectual disability, X-linked 49
Table 5. Recommended Surveillance for Individuals with CLCN4-Related Neurodevelopmental Disorder
System/Concern | Evaluation | Frequency |
|---|---|---|
Neurologic | Monitor those w/seizures as clinically indicated. | At each visit Assess for new manifestations incl seizures, changes in tone, mvmt disorders. Development |
Eyes | Per treating ophthalmologist | Per treating ophthalmologist or concerns raised by patient/caregiver Sensorineural |
hearing loss | Per treating audiologist | Per treating audiologist or concerns raised by patient/caregiver. Family/ |
Community | Assess family need for social work support (e.g., respite care, home nursing, other local resources) care coordination. | At each visit ADD = attention deficit disorder; OT = occupational therapy; PT = physical therapy |
Source: GeneReviews — "CLCN4-Related Neurodevelopmental Disorder"
Phenotype severity distribution: 7 always present features.
Estimated prevalence: <1 in 1,000,000 (VERY_RARE).
No clinical trials have been registered for intellectual disability, X-linked 49.
141 publications have been identified in PubMed for intellectual disability, X-linked 49. Research spans Basic Science / Preclinical (32%), Case Report / Case Series (16%), and Epidemiology / Natural History (16%).
Research Type | Count | % of Total |
|---|---|---|
Laboratory research | 45 | 32% |
Patient case studies | 23 | 16% |
Disease patterns and progression | 23 | 16% |
Testing and diagnosis research | 18 | 13% |
Research summaries | 17 | 12% |
Clinical study results | 13 | 9% |
New treatment approaches | 2 | 1% |
Duan H (2026). [PMID: 42244324](https://pubmed.ncbi.nlm.nih.gov/42244324/). *Zhong Nan Da Xue Xue Bao Yi Xue Ban*. [Review / Meta-Analysis]
Neto MI (2026). [PMID: 41631087](https://pubmed.ncbi.nlm.nih.gov/41631087/). *Cureus*. [Case Report / Case Series]
Lier J (2026). [PMID: 41853938](https://pubmed.ncbi.nlm.nih.gov/41853938/). *Journal of inherited metabolic disease*. [Diagnostic / Biomarker]
Thurman AJ (2026). [PMID: 39251531](https://pubmed.ncbi.nlm.nih.gov/39251531/). *J Autism Dev Disord*. [Diagnostic / Biomarker]
van de Stadt SIW (2026). [PMID: 41330739](https://pubmed.ncbi.nlm.nih.gov/41330739/). *Journal of inherited metabolic disease*. [Epidemiology / Natural History]
Ta D (2026). [PMID: 41535863](https://pubmed.ncbi.nlm.nih.gov/41535863/). *Orphanet J Rare Dis*. [Epidemiology / Natural History]
Liu N (2026). [PMID: 40884535](https://pubmed.ncbi.nlm.nih.gov/40884535/). *Journal of magnetic resonance imaging : JMRI*. [Diagnostic / Biomarker]
VanSickle EA (2026). [PMID: 41410504](https://pubmed.ncbi.nlm.nih.gov/41410504/). *American journal of medical genetics. Part A*. [Review / Meta-Analysis]
Samee N (2026). [PMID: 42193959](https://pubmed.ncbi.nlm.nih.gov/42193959/). *Cells*. [Basic Science / Preclinical]
Xu X (2026). [PMID: 41546782](https://pubmed.ncbi.nlm.nih.gov/41546782/). *Journal of molecular histology*. [Basic Science / Preclinical]
Data assembled from 7 of 12 sources · Last updated Sep 19, 2026, 6:44 AM UTC
Online Mendelian Inheritance in Man
European rare disease database
Genetic and Rare Diseases Info Center
To incl assessment of:; Gross motor fine motor skills; Mobility, ADL, need for adaptive devices; Need for PT (to improve gross motor skills) /or OT (to improve fine motor skills) Evaluate for joint hyperextensibility, pes planus, scoliosis, hypotonia. Gastrointestinal/ |
Feeding | Gastroenterology/nutrition/feedingeval | To incl eval of gastroesophageal reflux.; Consider need for nasogastric feeding or percutaneous gastrostomy depending on nutritional status.; Assess for constipation. |
Eyes | Ophthalmologiceval | Assessment of vision strabismus |
Hearing | Audiologic eval | Assess for hearing loss. |
Genetic counseling | By geneticsprofessionals1 | To inform affected persons their families re nature, MOI, implications of CLCN4-NDD in order to facilitate medical personal decision making Family support resources |
Treatment of Manifestations in Individuals with CLCN4-Related Neurodevelopmental Disorder Manifestation/Concern | Treatment | Considerations/Other |
DD/ID | See . | — |
Epilepsy | Standardized treatment w/ASM by experienced neurologist | While 5/25 persons w/epilepsy had some response to lamotrigine, more dedicated natural history studies are needed to clarify which ASMs are more (or less) effective.1; Education of parents/caregivers2 Psychiatric/ Behavioral |
Musculoskeletal | Orthopedics/ physical medicine rehab/ PT/OT | Monitor for joint hyperextensibility, pes planus, scoliosis, hypotonia. GI or growth concerns |
strabismus | Standard treatment(s) as recommended by ophthalmologist | Community vision services through early intervention or school district for those w/delayed visual maturation3 Hearing |