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Features include always present findings: Megalencephaly, Seizure, and Macrocephaly. 9 total HPO annotations.
Organ System | Phenotype Count | Example Features |
|---|---|---|
Brain and nerves | 6 | Mild intellectual disability, Seizure, Diffuse swelling of cerebral white matter |
Head and neck | 1 | Macrocephaly |
Age of onset: infancy.
The two phenotypes observed in individuals with megalencephalic leukoencephalopathy with subcortical cysts (MLC) are classic MLC and improving MLC. To date, approximately 500 individuals have been identified with biallelic pathogenic variants in MLC1 or HEPACAM, or heterozygous pathogenic variants in HEPACAM . To date, three individuals with heterozygous pathogenic variants in GPRC5B and classic MLC as well as two individuals with a biallelic pathogenic variant in AQP4 and improving MLC have been identified . The following description of the phenotypic features associated with this spectrum is based on these reports. Table 2. Megalencephalic Leukoencephalopathy with Subcortical Cysts (MLC): Comparison of Phenotypes by Select Features
Feature | Classic MLC | Improving MLC |
|---|---|---|
Macrocephaly, typically persistent | ~95% | ~55% |
Motor delays, initial | ~30% | ~15% |
Ataxia | ~80% | ~20% |
Pyramidal dysfunction | ~20% | ~5% |
Cognitive delays | ~70% | ~30% (mild ID) |
Autism spectrum disorder | ~10% |
Source: GeneReviews — "Megalencephalic Leukoencephalopathy with Subcortical Cysts"
MLC1 encodes modulator of VRAC current 1 (377 aa). Transmembrane protein mainly expressed in brain astrocytes that may play a role in transport across the blood-brain and brain-cerebrospinal fluid barriers. Highest expression in Brain Caudate basal ganglia (186.8 TPM) and Brain Nucleus accumbens basal ganglia (180.5 TPM).
Megalencephalic leukoencephalopathy with subcortical cysts 1 is caused by mutations in the MLC1 gene on chromosome 22.
MLC1 is classified as a druggable target (Ion Channel and Transporter categories) with score 0.0.
AQP4. Two sibs with biallelic AQP4 pathogenic variants have been reported with improving MLC similar to heterozygous HEPACAM-related improving MLC . GPRC5B. Three unrelated individuals with de novo heterozygous pathogenic variants in GPRC5B have been described . For these individuals, brain MRI presentation and clinical course are indistinguishable from MLC1-related classic MLC and biallelic HEPACAM-related classic MLC. HEPACAM. Most known biallelic and heterozygous HEPACAM pathogenic variants affect the extracellular or transmembrane domains of the protein .
Source: GeneReviews — "Megalencephalic Leukoencephalopathy with Subcortical Cysts"
Classic MLC. The penetrance of biallelic pathogenic variants in MLC1 or HEPACAM and heterozygous pathogenic variants in GPRC5B is expected to be complete. Improving MLC. The penetrance of heterozygous pathogenic variants in HEPACAM is reduced . The proportion of individuals with a heterozygous HEPACAM variant who exhibit or have exhibited clinical manifestations of improving MLC is unknown. The penetrance of biallelic pathogenic AQP4 variants is unknown.
Source: GeneReviews — "Megalencephalic Leukoencephalopathy with Subcortical Cysts"
Two phenotypes are observed in megalencephalic leukoencephalopathy with subcortical cysts (MLC): classic MLC and improving MLC.
Classic MLC should be suspected in individuals with the following clinical and brain imaging findings and family history.
Clinical findings
Macrocephaly with onset that is either congenital or within the first year of life
Normal or mildly delayed early development
Slow deterioration of motor functions with cerebellar ataxia and mild spasticity
Seizures
Dysarthria
Decline in cognitive function (occurs later and is typically milder than motor decline)
Behavioral problems in some individuals
Temporary exacerbation of signs and symptoms after minor head trauma
Imaging findings. Brain MRI features include the following abnormalities :
Source: GeneReviews — "Megalencephalic Leukoencephalopathy with Subcortical Cysts"
The differential diagnosis of macrocephaly and diffuse leukoencephalopathy is limited. Other disorders with white matter disease and swelling of the abnormal white matter are listed in . The clinical features and course of these disorders are usually different from those of megalencephalic leukoencephalopathy with subcortical cysts (MLC), and none of these disorders shares all the MRI features characteristic of MLC. Note: If the head circumference of an infant is well within the normal limits at age one year, it is highly unlikely that the infant has MLC.
Table 3.
Disorders of Interest in the Differential Diagnosis of Megalencephalic Leukoencephalopathy with Subcortical Cysts
Gene | Disorder | MOI | MRI Features
ASPA | Canavan disease | AR | In Canavan disease:
Source: GeneReviews — "Megalencephalic Leukoencephalopathy with Subcortical Cysts"
Genetic testing for MLC1 is available. Testing is considered confirmatory for diagnosis.
No approved treatments are currently available for megalencephalic leukoencephalopathy with subcortical cysts 1. The disease remains an area of unmet medical need.
Evaluations Following Initial Diagnosis To establish the extent of disease and needs in an individual diagnosed with megalencephalic leukoencephalopathy with subcortical cysts (MLC), the evaluations summarized (if not performed as part of the evaluation that led to the diagnosis) are recommended. Table 4. Megalencephalic Leukoencephalopathy with Subcortical Cysts: Recommended Evaluations Following Initial Diagnosis
System/Concern | Evaluation | Comment |
|---|---|---|
Neurologic | Neurologic assessment | Assess for macrocephaly (esp if progressive).; Brain MRI in those w/megalencephaly to assess white matter subcortical structures (See .); Consider EEG if seizures are a concern. |
Development | Developmental assessment | To incl physical, occupational, adaptive, cognitive, speech-language eval; Eval for early intervention/ special education Neuropsychological assessment |
Genetic counseling | By genetics professionals1 | To inform affected persons their families re nature, MOI, implications of MLC to facilitate medical personal decision making Family support resources |
Megalencephalic Leukoencephalopathy with Subcortical Cysts: Treatment of Manifestations Manifestation/Concern | Treatment | Considerations/Other |
Motor issues |
Source: GeneReviews — "Megalencephalic Leukoencephalopathy with Subcortical Cysts"
In individuals with classic MLC, minor head trauma may lead to temporary motor deterioration, seizures, or (rarely) coma. For this reason, contact sports and other activities with a high risk of head trauma should be avoided in affected individuals. Wearing a helmet should also be considered for situations associated with increased risk of head trauma.
Source: GeneReviews — "Megalencephalic Leukoencephalopathy with Subcortical Cysts"
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 — "Megalencephalic Leukoencephalopathy with Subcortical Cysts"
1 trial found
To monitor existing manifestations, the individual's response to supportive care, and the emergence of new manifestations, the evaluations summarized in are recommended. Table 6. Megalencephalic Leukoencephalopathy with Subcortical Cysts: Recommended Surveillance
System/Concern | Evaluation | Frequency |
|---|---|---|
Neurologic | Monitor those w/seizures as clinically indicated. | At each visit Assess for new manifestations such as seizures, progression of head growth, changes in tone, movement abnormalities. Brain MRI to assess for white matter changes, subcortical cyst progression, atrophy |
Development | Monitor developmental progress educational needs. | At each visit Eval w/developmental pediatrician |
Family/Community | Assess family need for social work support (e.g., palliative/respite care, home nursing, other local resources), care coordination, or follow-up genetic counseling if new questions arise (e.g., family planning). | At each visit |
Source: GeneReviews — "Megalencephalic Leukoencephalopathy with Subcortical Cysts"
Phenotype severity distribution: 3 always present features.
1 clinical trial registered, 1 recruiting. Interventions under study include other interventions. Research is primarily sponsored by academic and government institutions.
22 publications have been identified in PubMed for megalencephalic leukoencephalopathy with subcortical cysts 1. Research spans Basic Science / Preclinical (45%), Case Report / Case Series (32%), and Epidemiology / Natural History (9%).
Research Type | Count | % of Total |
|---|---|---|
Laboratory research | 10 | 45% |
Patient case studies | 7 | 32% |
Disease patterns and progression | 2 | 9% |
Research summaries | 1 | 5% |
Clinical study results | 1 | 5% |
New treatment approaches | 1 | 5% |
Sharma S (2026). [PMID: 41888865](https://pubmed.ncbi.nlm.nih.gov/41888865/). *Orphanet J Rare Dis*. [Basic Science / Preclinical]
Sartorelli J (2026). [PMID: 41483250](https://pubmed.ncbi.nlm.nih.gov/41483250/). *Neurol Sci*. [Epidemiology / Natural History]
Versaevel NRA (2026). [PMID: 42025183](https://pubmed.ncbi.nlm.nih.gov/42025183/). *Neuropediatrics*. [Clinical Trial Publication]
Pont-Espinós G (2026). [PMID: 41314544](https://pubmed.ncbi.nlm.nih.gov/41314544/). *J Biol Chem*. [Basic Science / Preclinical]
Kerst S (2026). [PMID: 41654199](https://pubmed.ncbi.nlm.nih.gov/41654199/). *Neurobiol Dis*. [Basic Science / Preclinical]
Bisseling Q (2026). [PMID: 41331492](https://pubmed.ncbi.nlm.nih.gov/41331492/). *Glia*. [Basic Science / Preclinical]
Lanciotti A (2026). [PMID: 41371307](https://pubmed.ncbi.nlm.nih.gov/41371307/). *Neurobiol Dis*. [Basic Science / Preclinical]
Potru M (2026). [PMID: 42037900](https://pubmed.ncbi.nlm.nih.gov/42037900/). *Cureus*. [Case Report / Case Series]
Sabbagh Q (2026). [PMID: 42063611](https://pubmed.ncbi.nlm.nih.gov/42063611/). *Neurol Genet*. [Basic Science / Preclinical]
Saibaba J (2025). [PMID: 40836748](https://pubmed.ncbi.nlm.nih.gov/40836748/). *J Assoc Physicians India*. [Case Report / Case Series]
Data assembled from 8 of 12 sources · Last updated Sep 20, 2026, 11:13 AM UTC
Online Mendelian Inheritance in Man
Seizures | ~65% | ~10% |
Brain MRI abnormalities | 100% | Initially 100%, but typically followed by improvement or normalization Data based on ID = intellectual disability; MLC = megalencephalic leukoencephalopathy with subcortical cysts Macrocephaly. Macrocephaly can be present at birth but more frequently develops during the first year of life. |
— |
Developmental delays | See . | — |
Epilepsy | Standardized treatment w/ASM by experienced neurologist or epileptologist | Many ASMs may be effective; none has been demonstrated effective specifically for this disorder.; Education of parents/caregivers1 Family/Community |