What you carry at this position in your DNA and what research says about it.
Epilepsy Drug Response: 8/10 evidence, 22 publications.
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Sample genotype (not yours): C/C
Typical Drug Response and Lower Seizure Risk
Standard maintenance doses of common anti-epileptic medications are typically effective. There is also a lower baseline risk of developing childhood febrile seizures.
What this genotype means: Standard maintenance doses of carbamazepine and phenytoin are typically effective; Lower baseline risk of childhood febrile seizures.
Sample genotype (not yours): C/T
Slightly Reduced Drug Response
Carbamazepine or phenytoin may be less effective for seizure control. There is also a slightly increased susceptibility to childhood febrile seizures.
What this genotype means: May respond less strongly to carbamazepine or phenytoin; Slightly increased risk of childhood febrile seizures.
Sample genotype (not yours): T/T
Reduced Drug Response and Seizure Risk
Carbamazepine and phenytoin are often significantly less effective, because of faster drug metabolism. There is also an increased risk of childhood febrile seizures.
What this genotype means: Often responds less strongly to carbamazepine and phenytoin; Increased risk of childhood febrile seizures; May respond more favorably to valproic acid.
Gene function and biological role
Gene Function: The SCN1A gene encodes the alpha subunit of the voltage-gated sodium channel Nav1.1, which is essential for transmitting electrical signals in the brain. This channel is highly expressed in inhibitory interneurons, helping to regulate and prevent over-excitation. Mutations or functional variations in this gene can dramatically alter brain excitability and susceptibility to seizures [1]. SCN1A is also the primary target for several widely used anti-epileptic medications [2]. Understanding variations in this gene helps clarify individual differences in drug response and seizure thresholds.
Variant Impact: The rs3812718 variant is a common single nucleotide polymorphism located in a conserved splice donor site of the SCN1A gene [3]. This genetic change alters the alternative splicing of exon 5, shifting the balance between the neonatal and adult forms of the sodium channel [3]. Specifically, the T allele disrupts splicing and reduces the expression of the neonatal isoform [1]. This molecular shift directly influences how the channel interacts with sodium-channel-blocking drugs [2]. Consequently, it serves as a key marker for predicting therapeutic drug dosages and seizure susceptibility.
Key Insight: This single-letter change in a non-coding region alters how the brain splices its sodium channels, shifting the ratio of neonatal to adult receptors. The same genetic variant that affects epilepsy drug dosage also influences the risk of childhood febrile seizures.
Location: SCN1A. Chromosome 2 · 2q24.3 · 166.1 Mb
Estimated prevalence by population
Global 27.3%; European 20.8%; African 42.5%; East Asian 19.6%; South Asian 19.7%; Americas 26.3%; Ashkenazi 21.2%; Finnish 21.4%; Middle Eastern 31.5%; Amish 17.3%.
Estimated CC genotype frequency.
Global 48.5%; European 49.6%; African 45.4%; East Asian 49.3%; South Asian 49.4%; Americas 50.0%; Ashkenazi 49.7%; Finnish 49.7%; Middle Eastern 49.3%; Amish 48.6%.
Estimated CT genotype frequency.
Global 24.2%; European 29.6%; African 12.1%; East Asian 31.1%; South Asian 30.9%; Americas 23.7%; Ashkenazi 29.1%; Finnish 28.9%; Middle Eastern 19.3%; Amish 34.0%.
Estimated TT genotype frequency.
Showing effects for C/C genotype
Pharmacogenomics
Antiepileptic & Mood-Stabilizer Response
Carbamazepine Response. Evidence: 8/10. Source: PMID 15805193. Typical Response.
Phenytoin Response. Evidence: 8/10. Source: PMID 15805193. Typical Response.
Valproic Acid Response. Evidence: 5/10. Source: PMID 37451178. Typical Response.
Neurology & Mental Health
Neurodevelopmental Traits
Febrile Seizures. Evidence: 8/10. Source: PMID 19289736. Typical Risk.
Showing effects for C/T genotype
Carbamazepine Response. Evidence: 8/10. Source: PMID 15805193. Slightly Higher Tolerance.
Phenytoin Response. Evidence: 8/10. Source: PMID 15805193. Higher Tolerance.
Valproic Acid Response. Evidence: 5/10. Source: PMID 37451178. Stronger Response.
Febrile Seizures. Evidence: 8/10. Source: PMID 19289736. Increased Risk.
Showing effects for T/T genotype
Carbamazepine Response. Evidence: 8/10. Source: PMID 15805193. Higher Tolerance.
What this genotype means for the people who carry it
Sample genotype: CC (Homozygous)
Standard splicing of the SCN1A gene allows for balanced expression of both neonatal and adult sodium channel isoforms in the brain [1]. This molecular balance is associated with a typical response to first-line anti-epileptic drugs like carbamazepine and phenytoin [2]. Clinical studies show that standard maintenance doses are often sufficient to achieve seizure control without requiring unusually high escalation [2]. Furthermore, this genetic profile is associated with a lower risk of experiencing febrile seizures during childhood compared to those carrying the variant allele [3]. Having a balanced ratio of these channel isoforms helps maintain stable electrical signaling across neural networks. While medication response is highly complex and influenced by many clinical factors, this genetic marker suggests a favorable profile for standard sodium channel blockers [2]. Standard clinical guidelines often consider this genetic background when evaluating drug efficacy. It is important to discuss any medication concerns directly with a healthcare provider before making changes.
Standard maintenance doses of carbamazepine and phenytoin are typically effective; Lower baseline risk of childhood febrile seizures.
Sample genotype: CT (Heterozygous)
Alternative splicing of the SCN1A gene is altered by the presence of one copy of the variant T allele [1]. This alteration reduces the proportion of the neonatal sodium channel isoform in the brain, which can affect drug binding [1]. Clinical evidence indicates that some individuals with this profile respond slightly less strongly to carbamazepine or phenytoin for seizure control [2]. The presence of the T allele is also linked to an increased susceptibility to febrile seizures during childhood [3]. This shift in channel expression can subtly alter the threshold for electrical activity in the brain. However, some research suggests a potentially better response to alternative treatments like valproic acid [4]. Because multiple genetic and environmental factors influence drug efficacy, these findings serve as a guide rather than a definitive prediction. Any adjustments to medication dosage or selection should always be managed by a qualified medical professional.
May respond less strongly to carbamazepine or phenytoin; Slightly increased risk of childhood febrile seizures.
Sample genotype: TT (Homozygous)
Altered splicing of the SCN1A gene occurs when two copies of the variant T allele are present, severely reducing the neonatal sodium channel isoform [1]. This molecular shift alters how the channel interacts with common anti-epileptic medications [1]. Multiple clinical studies show that this profile is strongly associated with needing higher maintenance doses of carbamazepine and phenytoin to achieve therapeutic levels [2]. The variant is also linked to faster metabolism of carbamazepine, which can lower its active concentration in the body [3]. In addition to dosage differences, this genotype is associated with an increased risk of developing childhood febrile seizures [4]. This significant reduction in the neonatal isoform alters the overall excitability of neural pathways. Conversely, some data suggest these individuals may respond more favorably to valproic acid therapy [5]. These genetic insights can help clinicians tailor treatment strategies, but they do not replace standard clinical monitoring. All treatment decisions must be made in consultation with a healthcare provider.
Often responds less strongly to carbamazepine and phenytoin; Increased risk of childhood febrile seizures; May respond more favorably to valproic acid.
Variants with shared genetic architecture
rs2298771 · SCN1A Gene · Chr 2 · Epilepsy Drug Response
rs2273697 · ABCC2 Gene · Chr 10 · Carbamazepine Side Effects
rs28399504 · CYP2C19 Gene · Chr 10 · Drug Metabolism
A splice site variant in the sodium channel gene SCN1A confers risk of febrile seizures.
Content updated August 2026.
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