KCNT1 p.Pro237=
c.711C>G · rs117286274 · VCV129367
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 7 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.03%, nfe)
Conditions
3
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -20 | GERP -3.9 |
| Overall | ||
| CADD | 0.242 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.03%
European (non-Finnish) · 23,991/1,179,932 alleles
Filtering AF
2.01%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2%
Overall
1.67%
26,922/1,611,700 alleles · low-frequency
exomes 25,085/1,459,592 · genomes 1,837/152,108 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 2.03% | 49 |
| Finnishnot grpmax-eligible | 1.66% | 60 |
| Remaining individualsnot grpmax-eligible | 1.48% | 68 |
| Admixed American | 0.93% | 108 |
| Ashkenazi Jewishnot grpmax-eligible | 0.564% | 177 |
| African / African-American | 0.281% | 356 |
| Middle Eastern | 0.214% | 466 |
| Amishnot grpmax-eligible | 0.11% | 912 |
| South Asian | 0.0362% | 2,759 |
| East Asian | 0.00223% | 44,828 |
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.Pro237=
- Coding
- c.711C>G
- MANE Select
- NM_020822
- dbSNP
- rs117286274
- Type
- single nucleotide variant
- Location
- chr9:135757333 (GRCh38)
- Gene constraint
- LOEUF 0.682 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 74.94 · 6 PDB
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-pro237 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown