KCNN3 p.Phe466=
c.1398C>T · VCV4913463
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
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 5.1 | GERP 1.5, phastCons 1 |
| Overall | ||
| CADD | 9.582 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- KCNN3
- Protein
- p.Phe466=
- Coding
- c.1398C>T
- MANE Select
- NM_002249
- Type
- single nucleotide variant
- Location
- chr1:154772025 (GRCh38)
- Gene constraint
- LOEUF 0.379 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 68.54
Similar variants
- KCNN3 p.Ala536Thr Pathogenic/Likely pathogenic ★★ same type
- KCNN3 p.Arg224Gln Uncertain significance ★★ ⚠ same type
- KCNN3 p.Glu204Gly Uncertain significance ★★ ⚠ same type
- KCNN3 p.Val716Phe Uncertain significance ★★ ⚠ same type
- KCNN3 c.1702-3T>C Likely benign ★★ same type
- KCNN3 p.Ala229= Likely benign ★★ same type
- KCNN3 p.Asn349= Benign ★★ same type
- KCNN3 p.Glu381Gln Likely benign ★★ same type
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/kcnn3-p-phe466 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown