Benign familial infantile epilepsy: genes and variants

Genes linked to Benign familial infantile epilepsy

• SCN2A: Sodium channel protein type 2 subunit alpha

  The protein forms Nav1.2, a voltage-gated sodium channel that carries sodium current during neuronal action potentials. By shaping neuronal excitability and signal propagation, it supports brain circuits involved in development, learning, and seizure susceptibility.

  6 disease-causing and 0 uncertain variants in SCN2A are linked to Benign familial infantile epilepsy.

• PRRT2: Proline-rich transmembrane protein 2

  It modulates presynaptic neurotransmitter release and neuronal excitability through interactions with SNARE machinery and ion channels. Haploinsufficiency commonly causes paroxysmal kinesigenic dyskinesia, self-limited infantile seizures, or the combined infantile-convulsions-and-choreoathetosis phenotype.

  0 disease-causing and 0 uncertain variants in PRRT2 are linked to Benign familial infantile epilepsy.

Known disease-causing variants in Benign familial infantile epilepsy

Same protein, different disease

• Seizures, benign familial infantile, 3 is also caused by SCN2A variants; they fall mostly in different places as the Benign familial infantile epilepsy variants (167 disease-causing).
• Complex neurodevelopmental disorder is also caused by SCN2A variants; they fall mostly in different places as the Benign familial infantile epilepsy variants (22 disease-causing).
• Episodic ataxia type 2 is also caused by SCN2A variants; they fall mostly in different places as the Benign familial infantile epilepsy variants (15 disease-causing).
• West syndrome is also caused by SCN2A variants; they fall mostly in different places as the Benign familial infantile epilepsy variants (11 disease-causing).
• Infantile spasms is also caused by SCN2A variants; they fall mostly in different places as the Benign familial infantile epilepsy variants (3 disease-causing).

Diseases related to Benign familial infantile epilepsy

• Seizures, benign familial infantile, 3, also linked to PRRT2 and SCN2A
• Amyotrophic lateral sclerosis, also linked to SCN2A
• Episodic ataxia type 2, also linked to SCN2A
• Cardiac arrhythmia, also linked to SCN2A
• Complex neurodevelopmental disorder, also linked to SCN2A
• Epilepsy, also linked to SCN2A
• West syndrome, also linked to SCN2A
• Episodic kinesigenic dyskinesia, also linked to PRRT2
• Self-limited epilepsy with centrotemporal spikes, also linked to SCN2A
• Focal epilepsy, also linked to SCN2A
• Infantile spasms, also linked to SCN2A
• Genetic developmental and epileptic encephalopathy, also linked to SCN2A

Frequently asked questions

Which genes are linked to Benign familial infantile epilepsy?

In CATVariant, Benign familial infantile epilepsy is linked to 2 analyzed proteins: SCN2A (Sodium channel protein type 2 subunit alpha) and PRRT2 (Proline-rich transmembrane protein 2).

How many genetic variants are linked to Benign familial infantile epilepsy?

20 variants: 6 are classified as disease-causing (pathogenic or likely pathogenic) in ClinVar and 0 are of uncertain significance or have conflicting reports.

Which uncertain variants in Benign familial infantile epilepsy look disease-causing?

None of the uncertain variants currently reaches the likely-pathogenic range on computable evidence alone.

About this data

Variant–disease links come from ClinVar, Open Targets and UniProt, pooled from the latest public CATVariant analysis of each human protein. Evidence scores use the ACMG/AMP Bayesian points scale with computable criteria only (position among known disease variants, rarity in gnomAD, calibrated predictors, deep mutational scanning); there is no family or patient data, so they prioritise variants for expert review and never classify them.

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