KCNT1 p.Ser79=
c.237C>T · rs749179872 · VCV386190
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00897%, afr)
Conditions
2
developmental and epileptic encephalopathy, 14
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1 | GERP -2.5 |
| Overall | ||
| CADD | 12.29 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00897%
African / African-American · 6/66,926 alleles
Filtering AF
0.00381%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00261%
Overall
0.000484%
7/1,445,656 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00897% | 11,154 |
| European (non-Finnish) | 9.21e-05% | 1,086,202 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- KCNT1
- Protein
- p.Ser79=
- Coding
- c.237C>T
- MANE Select
- NM_020822
- dbSNP
- rs749179872
- Type
- single nucleotide variant
- Location
- chr9:135714703 (GRCh38)
- Gene constraint
- LOEUF 0.682 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 74.94 · 6 PDB
- Residue 79
- an α-helix
Similar variants
- KCNT1 p.Ala477Thr Pathogenic/Likely pathogenic ★★ same condition
- KCNT1 p.Ala934Ser Pathogenic/Likely pathogenic ★★ same condition
- KCNT1 p.Ala934Thr Pathogenic ★★ same condition
- KCNT1 p.Ala966Thr Pathogenic/Likely pathogenic ★★ same condition
- KCNT1 p.Arg262Gln Pathogenic/Likely pathogenic ★★ ⚠ same condition
- KCNT1 p.Arg356Trp Pathogenic/Likely pathogenic ★★ ⚠ same condition
- KCNT1 p.Arg398Gln Pathogenic/Likely pathogenic ★★ ⚠ same condition
- KCNT1 p.Arg428Gln Pathogenic ★★ ⚠ same condition
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/kcnt1-p-ser79 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown