KCNN2 p.Ser151=
c.453G>T · VCV4872353
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0245%, nfe)
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 0.12 | GERP -1.7, phastCons 0.96 |
| Overall | ||
| CADD | 5.785 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0245%
European (non-Finnish) · 122/498,112 alleles
Filtering AF
0.0209%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0196%
Overall
0.0179%
136/759,094 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0245% | 4,083 |
| Admixed American | 0.0234% | 4,278 |
| Remaining individualsnot grpmax-eligible | 0.00912% | 10,961 |
| African / African-American | 0.00743% | 13,450 |
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
- KCNN2
- Protein
- p.Ser151=
- Coding
- c.453G>T
- MANE Select
- NM_021614
- Type
- single nucleotide variant
- Location
- chr5:114362592 (GRCh38)
- Gene constraint
- LOEUF 0.661 · pLI 0.07 (gnomAD)
- Structure
- AlphaFold pLDDT 77.98 · 16 PDB
Similar variants
- KCNN2 p.Gly574Ser Pathogenic ★★ same type
- KCNN2 p.Tyr573Cys Pathogenic/Likely pathogenic ★★ same type
- KCNN2 p.Arg233Leu Uncertain significance ★★ ⚠ same type
- KCNN2 p.Asn412Ser Uncertain significance ★★ ⚠ same type
- KCNN2 p.Gln15Ter Uncertain significance ★★ same type
- KCNN2 p.Ile730Val Uncertain significance ★★ ⚠ same type
- KCNN2 p.Ile744Met Uncertain significance ★★ ⚠ same type
- KCNN2 p.Lys332Arg Uncertain significance ★★ ⚠ 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/kcnn2-p-ser151 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown