KSR2 p.Pro261=
c.783G>A · VCV3358679
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00186%, amr)
Conditions
1
KSR2-related disorder
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 -11 | GERP -3.9 |
| Overall | ||
| CADD | 1.091 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00186%
Admixed American · 1/53,866 alleles
Overall
0.000128%
2/1,564,060 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00186% | 53,866 |
| African / African-American | 0.00136% | 73,412 |
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
- KSR2
- Protein
- p.Pro261=
- Coding
- c.783G>A
- MANE Select
- NM_173598
- Type
- single nucleotide variant
- Location
- chr12:117761214 (GRCh38)
- Gene constraint
- LOEUF 0.318 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 61.22 · 9 PDB
- Residue 261
- the 'disordered' region
Disease context
KSR2-related disorder
Similar variants
- KSR2 p.Arg745Gln Uncertain significance ★★ ⚠ same condition
- KSR2 p.Gln665His Uncertain significance ★★ ⚠ same condition
- KSR2 p.Leu546Pro Uncertain significance ★★ ⚠ same condition
- KSR2 p.Pro171Ser Uncertain significance ★★ ⚠ same condition
- KSR2 c.1802+2T>A Likely pathogenic ★ same condition
- KSR2 p.Arg192Leu Uncertain significance ★ ⚠ same condition
- KSR2 p.Arg296Leu Uncertain significance ★ ⚠ same condition
- KSR2 p.Arg643Gln Uncertain significance ★ ⚠ 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/ksr2-p-pro261 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown