KCNT2
Chr 1ADpotassium sodium-activated channel subfamily T member 2
Also known as: DEE57, EIEE57, KCa4.2, KNa1.2, SLICK, SLO2.1
The protein functions as a sodium-activated and chloride-activated potassium channel that regulates neuronal excitability by producing outward rectifier K+ currents across the plasma membrane. Mutations cause developmental and epileptic encephalopathy 57, characterized by early-onset seizures and developmental delays. The condition follows autosomal dominant inheritance, and the gene is highly constrained against loss-of-function variants (LOEUF 0.374).
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
More LoF-intolerant than ~75% of genes
Highly missense-constrained (top ~0.1%)
This gene has evidence for multiple mechanisms of pathogenicity (gain-of-function and dominant-negative). Both the Badonyi & Marsh prediction and the broader genomic evidence point to gain-of-function as the predominant mechanism. Different variants in this gene may act through different mechanisms — interpret in context of the specific variant.
Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.
Literature Evidence
Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.
ClinVar Variant Classifications
0 submitted variants in ClinVar
Protein Context — Lollipop Plot
KCNT2 · protein map & ClinVar variants
Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.
3D Protein StructureAlphaFold
External Resources
Links to major genomics databases and tools
Clinical Trials
Active and recruiting trials from ClinicalTrials.gov
No active trials found for this gene.
Search ClinicalTrials.gov →External Resources
Links to major genomics databases and tools