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Features include always present findings: Macrocephaly; and very common findings: Seizure and Mental deterioration. 19 total HPO annotations.
Organ System | Phenotype Count | Example Features |
|---|---|---|
Brain and nerves | 13 | Brain shrinkage (cerebral atrophy), Difficulty swallowing (dysphagia), Delayed speech and language development |
Muscles | 2 | Brain shrinkage (cerebral atrophy), Shrinkage of the cerebellum (cerebellar atrophy) |
Arms and legs | 2 | Lower limb spasticity, Upper limb spasticity |
Digestive system | 1 | Difficulty swallowing (dysphagia) |
Head and neck | 1 | Macrocephaly |
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% | ~25% |
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. |
Source: GeneReviews — "Megalencephalic Leukoencephalopathy with Subcortical Cysts"
HEPACAM encodes hepatic and glial cell adhesion molecule (416 aa). Involved in regulating cell motility and cell-matrix interactions. May inhibit cell growth through suppression of cell proliferation. Highest expression in Brain Cortex (57.6 TPM) and Brain Caudate basal ganglia (54.5 TPM).
Megalencephalic leukoencephalopathy with subcortical cysts 2A is caused by mutations in the HEPACAM gene on chromosome 11.
HEPACAM is classified as a druggable target (Transporter and Tumor Suppressor 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 HEPACAM is available. Testing is considered confirmatory for diagnosis.
No approved treatments are currently available for megalencephalic leukoencephalopathy with subcortical cysts 2A. 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"
View trials for megalencephalic leukoencephalopathy with subcortical cysts 2A
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: 1 always present feature, 2 very common features, 7 common features.
No clinical trials have been registered for megalencephalic leukoencephalopathy with subcortical cysts 2A.
3 publications have been identified in PubMed for megalencephalic leukoencephalopathy with subcortical cysts 2A. Kisho has analyzed 2 by research type. Research spans Basic Science / Preclinical (50%) and Gene Therapy / Novel Therapeutics (50%).
Lewis RW (2025). [PMID: 40894676](https://pubmed.ncbi.nlm.nih.gov/40894676/). *bioRxiv*. [Basic Science / Preclinical]
Brao A (2025). [PMID: 40051162](https://pubmed.ncbi.nlm.nih.gov/40051162/). *Mol Ther*. [Gene Therapy / Novel Therapeutics]
Data assembled from 7 of 12 sources · Last updated Sep 19, 2026, 9:40 PM UTC
Online Mendelian Inheritance in Man
Genetic and Rare Diseases Info Center
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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 |