Dravet Syndrome — SCN1A loss-of-function producing severe early-onset epilepsy where the most commonly prescribed anti-seizure drugs make the condition worse.
Whole genome sequencing reads the complete SCN1A gene sequence, detecting mosaic and deep intronic variants that cause Dravet syndrome in genetically unresolved patients — and identifies the pharmacogenomic contraindications that determine which drugs can and cannot be used safely.
Dravet Syndrome
Dravet syndrome (DS) — formerly severe myoclonic epilepsy of infancy (SMEI) — is a severe developmental and epileptic encephalopathy with onset in the first year of life, typically in a previously healthy infant. The condition is characterized by prolonged febrile and afebrile seizures (often clonic or hemiclonic), subsequent polymorphic seizure types (myoclonic, absence, focal), and progressive developmental slowing beginning in the second year of life. Dravet syndrome has a population prevalence of approximately 1 in 15,000-22,000 births and accounts for approximately 3-8% of epilepsies with onset in the first three years of life.
Pathogenic or likely pathogenic SCN1A variants are identified in approximately 70-85% of patients meeting clinical Dravet syndrome diagnostic criteria. SCN1A encodes the Nav1.1 alpha subunit of voltage-gated sodium channels, which is critical for inhibitory interneuron function. Loss-of-function disrupts GABAergic interneuron firing, producing cortical disinhibition and hyperexcitability. Approximately 95% of pathogenic SCN1A variants in Dravet syndrome are de novo (not inherited from a parent). Pathogenic variant types include truncating variants (nonsense, frameshift — approximately 40%), splice site variants, and missense variants (approximately 40%); large deletions or duplications account for approximately 2-3% and require copy number variant analysis for detection.
The SCN1A genotype has direct, life-critical pharmacogenomic implications. Sodium channel-blocking anti-seizure medications — including lamotrigine, carbamazepine, oxcarbazepine, phenytoin, and vigabatrin — worsen seizure control and can precipitate epileptic encephalopathy in SCN1A-positive patients by further reducing Nav1.1 function in inhibitory interneurons. This contraindication applies regardless of variant specific type. Treatments with established evidence in Dravet syndrome include valproate, clobazam, topiramate, stiripentol, and (in eligible patients) fenfluramine and cannabidiol (Epidiolex). An unresolved or misattributed diagnosis means the wrong drugs may be prescribed during the critical window when drug selection most affects long-term developmental outcome.
Approximately 15-30% of patients with a clinical Dravet syndrome diagnosis are SCN1A-negative on standard panel testing. A proportion of these carry deep intronic, mosaic, or structural SCN1A variants detectable by whole genome sequencing.
Standard epilepsy panels detect coding SCN1A variants. They miss mosaic mutations, deep intronic splicing variants, and large structural rearrangements that account for a clinically significant fraction of SCN1A-negative Dravet syndrome.
Mosaic SCN1A variants require sequencing depth and breadth that panels cannot provide
Somatic mosaicism — where the SCN1A pathogenic variant is present in only a subset of cells — explains a portion of clinical Dravet syndrome cases with negative panel results. Mosaic variants at 10-30% allele frequency can be missed by standard panel sequencing, where clinical sensitivity is optimized for germline heterozygous variants at ~50% allele fraction. Studies using deep whole genome sequencing have identified mosaic SCN1A variants in 4-8% of panel-negative Dravet syndrome patients. Deep intronic SCN1A variants that create cryptic splice sites represent an additional category of panel-invisible pathogenic variants. Both require the breadth and depth of whole genome sequencing for reliable detection.
The SCN1A result determines which anti-seizure drugs are safe to prescribe
In Dravet syndrome, drug class selection is not a matter of optimization — it is a matter of safety. Sodium channel blockers are contraindicated in SCN1A loss-of-function and have been documented to trigger seizure worsening, status epilepticus, and in some cases acute encephalopathic deterioration. Multiple case series have documented patients with Dravet syndrome who worsened substantially after initiation of lamotrigine or carbamazepine before the genetic diagnosis was established. Confirming an SCN1A pathogenic variant provides the actionable genetic basis for avoiding sodium channel blockers and initiating evidence-based DS-specific therapies — a decision that acutely affects seizure burden and developmental trajectory.
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Common questions about whole genome sequencing.
What is the difference between whole genome sequencing and a targeted genetic test?
Targeted genetic tests — including standard hereditary cancer panels — read a pre-defined list of known variants in a specific set of genes. They are designed to find what they already know to look for. Whole genome sequencing reads your entire genome: all 6 billion base pairs, every gene, every region between genes. A Mayo Clinic study published in JAMA Oncology found that standard testing guidelines missed more than half of patients with inherited cancer mutations. Genome Test does not have a fixed list.
What will I receive when my results are ready?
Your Dante Genome delivers 200+ physician-ready reports organized by clinical category — hereditary cancer, cardiac conditions, rare diseases, pharmacogenomics, carrier status, and more. Reports are delivered to your secure Genome Manager and are formatted for direct clinical use. Your genome data is permanently retained and re-analyzed automatically as science advances.
What happens if a clinically significant variant is found?
If a pathogenic or likely-pathogenic variant is identified, it will be clearly flagged in your physician-ready report with clinical context, published evidence, and recommended next steps. We recommend sharing any clinically significant finding with your physician or a genetic counselor, who can guide decisions about surveillance, risk reduction, or cascade testing for family members.
How is this different from a consumer DNA test like 23andMe or AncestryDNA?
Consumer DNA tests use genotyping chips that read less than 0.1% of your genome — a tiny pre-selected set of common variants. They are optimized for ancestry and population-level traits, not clinical genetic findings. The Dante Genome Test sequences 100% of your genome at 30X coverage, the same standard used in clinical diagnostic settings. The two tests are not comparable in scope, methodology, or clinical utility.
How long does it take to get results, and how are they delivered?
Your collection kit ships within 48 hours of ordering. Once your sample arrives at our CLIA-certified laboratory, sequencing and analysis takes 6–8 weeks. Results are delivered securely to your Genome Manager, where you can access your reports, share them with your physician, and receive automatic updates as new findings are validated against your genome.
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