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Features include always present findings: Small face, Low muscle tone (hypotonia), Problems with involuntary body functions (abnormal autonomic nervous system physiology), and Focal-onset seizure; and common findings: Focal impaired awareness seizure. 13 total HPO annotations.
Organ System | Phenotype Count | Example Features |
|---|---|---|
Brain and nerves | 9 | Bilateral tonic-clonic seizure, Borderline intellectual disability, Delayed speech and language development |
SCN3A function has not been fully characterized.
Epilepsy, familial focal, with variable foci 4 is associated with mutations in the SCN3A gene on chromosome 2.
The most common recurrent SCN3A pathogenic variant is , identified in 26% of individuals with SCN3A-NDD [, , , , ]. The phenotype associated with this variant is relatively homogeneous, severe, and with poor outcomes from a developmental and epilepsy management perspective. Clinical features include:
Clinical diagnostic criteria for SCN3A-related neurodevelopmental disorder (SCN3A-NDD) have not been published.
SCN3A-NDD should be considered in individuals with the following clinical features, seizure types, brain MRI findings, and/or family history.
Clinical features
Source: GeneReviews — "SCN3A-Related Neurodevelopmental Disorder"
No approved treatments are currently available for epilepsy, familial focal, with variable foci 4. The disease remains an area of unmet medical need.
Treatment of SCN3A-related neurodevelopmental disorder (SCN3A-NDD) is best led by a physician familiar with pharmacotherapy of treatment-resistant epilepsy, such as a pediatric neurologist or pediatric epileptologist. No clinical practice guidelines for SCN3A-NDD have been published. Evaluations Following Initial Diagnosis To establish the extent of disease and needs in an individual diagnosed with SCN3A-NDD, the evaluations summarized (if not performed as part of the evaluation that led to the diagnosis) are recommended. Table 4. Recommended Evaluations Following Initial Diagnosis in Individuals with SCN3A-Related Neurodevelopmental Disorder
Table 6. Recommended Surveillance for Individuals with SCN3A-Related Neurodevelopmental Disorder
System/Concern |
|---|
No clinical trials have been registered for epilepsy, familial focal, with variable foci 4.
2 publications have been identified in PubMed for epilepsy, familial focal, with variable foci 4. Research spans Basic Science / Preclinical (50%) and Gene Therapy / Novel Therapeutics (50%).
Wang PY (2026). [PMID: 41725720](https://pubmed.ncbi.nlm.nih.gov/41725720/). *Frontiers in neurology*. [Gene Therapy / Novel Therapeutics]
Langhammer F (2025). [PMID: 39849855](https://pubmed.ncbi.nlm.nih.gov/39849855/). *Human molecular genetics*. [Basic Science / Preclinical]
Data assembled from 6 of 12 sources · Last updated Sep 20, 2026, 12:19 PM UTC
Online Mendelian Inheritance in Man
Head and neck | 2 | Microcephaly, Small face |
Muscles | 1 | Low muscle tone (hypotonia) |
SCN3A-related neurodevelopmental disorder (SCN3A-NDD) encompasses a spectrum of clinical severity associated with epilepsy and/or malformation of cortical development (MCD). Affected individuals may have developmental and epileptic encephalopathy (DEE) (i.e., intractable seizures with developmental delays associated with ongoing epileptiform EEG activity) with or without MCD, or MCD with or without mild focal epilepsy. To date, 38 individuals from 31 families have been identified with a pathogenic variant in SCN3A [, , , , , , , , , , ]. The following summarizes the clinical findings in these individuals. Table 2. Select Features of SCN3A-Related Neurodevelopmental Disorder
Feature | Proportion ofPersons w/Feature | Comment |
|---|---|---|
Developmental delay | 38/38 (100%) | Severity ranges widely from mild isolated speech delay to profound developmental delays. |
Malformation of cortical development | 31/38 (82%) | — |
Epilepsy | 26/38 (68%) | A common but not obligatory feature |
Autonomic dysregulation | 40%-60% | Features typically assoc w/DEE Infantile hypotonia |
Oromotor dysfunction | 13/32 (41%) | Most prominent in those w/o DEE |
Progressive microcephaly | 12/30 (40%) | Features typically assoc w/DEE Hyperkinetic movement disorder |
Source: GeneReviews — "SCN3A-Related Neurodevelopmental Disorder"
Profound developmental delay/ intellectual disability (in 10/10 individuals; 100%)
Neonatal onset intractable seizures (median onset 2 weeks) (8/9; 89%)
Multiple seizure types, often generalized tonic seizures
Diffuse, bilateral polymicrogyria (10/10; 100%)
Microcephaly (7/9;78%)
Paroxysmal ictal and non-ictal autonomic dysregulation (4/9; 44%)
A clear genotype-phenotype correlation between other variants or classes of variants has not yet been established.
Source: GeneReviews — "SCN3A-Related Neurodevelopmental Disorder"
The phenotype(s) observed in SCN3A-related neurodevelopmental disorder (SCN3A-NDD) are not sufficient to diagnose an SCN3A-NDD without genetic testing, as other conditions may be associated with clinical features and neuroimaging findings within the same range of phenotypes. Epilepsy. The epilepsy phenotype of SCN3A-NDD cannot be definitively distinguished from other causes of early-infantile epileptic encephalopathies (80 genetic causes have been identified; see OMIM Phenotypic Series). Malformation of cortical development (MCD). A key element of the differential diagnosis is to distinguish SCN3A-NDD from other causes of MCD as these may be associated with a different clinical course and/or mode of inheritance. Other causes of MCD include:
Source: GeneReviews — "SCN3A-Related Neurodevelopmental Disorder"
Genetic testing for SCN3A is available. Testing is considered confirmatory for diagnosis.
System/Concern | Evaluation | Comment |
|---|---|---|
Neurologic | Neurologic eval | To incl brain MRI EEG; Consider video EEG to assess seizure frequency, define seizure type(s), assess for autonomic dysfunction.1; To incl assessment for hyperkinetic movements |
Development | Developmental assessment | To incl motor, adaptive, cognitive, speech-language eval; Eval for early intervention/ special education Psychiatric/ |
Behavioral | Neuropsychiatric eval | In persons age 12 mos: screen for concerns incl sleep disturbances, ADHD, anxiety, /or findings suggestive of ASD. |
Musculoskeletal | Orthopedics/ physical medicine rehab/ PT OT eval | To incl assessment of:; Gross motor fine motor skills; Contractures kyphoscoliosis; Mobility, activities of daily living, need for adaptive devices; Need for PT (to improve gross motor skills) /or OT (to improve fine motor skills) Gastrointestinal/ |
Feeding | Gastroenterology/ nutrition/ feeding team eval | To incl eval of oromotor dysfunction nutritional status; Consider eval for gastrostomy tube placement in persons w/dysphagia /or aspiration risk. |
Eyes | Ophthalmologic eval | To assess for vision Genetic |
counseling | By genetics professionals2 | To obtain a pedigree inform affected persons their families re nature, MOI, implications of SCN3A-NDD to facilitate medical personal decision making Family support resources |
Treatment of Manifestations in Individuals with SCN3A-Related Neurodevelopmental Disorder Manifestation/Concern | Treatment | Considerations/Other |
Epilepsy | Empiric treatment of seizures w/standard ASM1 | Incl lacosamide, phenytoin, carbamazepine2,3; No one ASM has been shown to be more efficacious than another.; Education of parents/caregivers4 Hyperkinetic |
movements | Standard treatment per neurologist | Autonomic dysfunction |
DD/ID | See . | — |
Spasticity | Orthopedics/ physical medicine rehab/ PT OT incl stretching to help avoid contractures falls | Consider need for positioning mobility devices, disability parking placard. Poor weight |
gain/ FTT | Feeding therapy; gastrostomy tube placement may be required for persistent feeding issues. | Low threshold for clinical feeding eval /or radiographic swallowing study if clinical signs or symptoms of dysphagia Central visual |
impairment | No specific treatment; early intervention to stimulate visual development | Family/ Community |
Source: GeneReviews — "SCN3A-Related Neurodevelopmental Disorder"
There is NO evidence that:
Specific anti-seizure medications can worsen seizures associated with SCN3A-NDD;
Sleep deprivation or fever exacerbates seizures associated with SCN3A-NDD.
Source: GeneReviews — "SCN3A-Related Neurodevelopmental Disorder"
Therapeutic trials of anti-seizure medications that target sodium channels may be indicated in cases of severe, treatment-resistant epilepsy or epileptic encephalopathy associated with SCN3A-NDD based on theoretic considerations [, , , ]. 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 — "SCN3A-Related Neurodevelopmental Disorder"
View trials for epilepsy, familial focal, with variable foci 4
Evaluation
Frequency |
|---|
Growth | Measurement of weight, length/height, head circumference | At each visit Neurologic1 |
Eyes | Ophthalmology eval to assess for visual impairment | Annually Miscellaneous/ |
Other | Assess family need for social work support (e.g., palliative/respite care, home nursing, other local resources) care coordination. | At each visit OT = occupational therapy; PT = physical therapy 1. Serial neurologic examination and neurodevelopmental assessment is appropriate. 2. EEG monitoring is appropriate when new or different seizure type(s) are suspected. |
Source: GeneReviews — "SCN3A-Related Neurodevelopmental Disorder"
Phenotype severity distribution: 4 always present features, 1 common feature.