KCNN2 p.Pro39Ser
c.115C>T · VCV4281560
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Not reported
no allele count reported in gnomAD v4.1 (AN 173,996)
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 1.1 | GERP -0.39, phastCons 1 |
| Regional constraint | o/e 1.47 | unconstrained · MANE · 967 bp · p 3.7e-14 · regional, not allelic |
| Overall | ||
| CADD | 17.71 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
No allele count reported in gnomAD v4.1 (AN 173,996). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- KCNN2
- Protein
- p.Pro39Ser
- Coding
- c.115C>T
- MANE Select
- NM_021614
- Type
- single nucleotide variant
- Location
- chr5:114362254 (GRCh38)
- Gene constraint
- LOEUF 0.661 · pLI 0.07 (gnomAD)
- Structure
- AlphaFold pLDDT 77.98 · 16 PDB
- Residue 39
- the 'disordered' region
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-pro39ser (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown