MAPKAPK3 p.Thr40=
c.120C>A · VCV4774662
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00017%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>T here scores Δ0.29 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -4.1 | GERP -5.2 |
| Overall | ||
| CADD | 5.943 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00017%
European (non-Finnish) · 2/1,179,804 alleles
Filtering AF
2.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000124%
2/1,613,368 alleles · very rare
exomes 2/1,461,080 · genomes 0/152,288 · joint denominator
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
- MAPKAPK3
- Protein
- p.Thr40=
- Coding
- c.120C>A
- MANE Select
- NM_001243925
- Type
- single nucleotide variant
- Location
- chr3:50617685 (GRCh38)
- Gene constraint
- LOEUF 0.943 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 83.10 · 5 PDB
- Residue 40
- an α-helix
Similar variants
- MAPKAPK3 p.Ala181Ser Uncertain significance ★★ ⚠ same type
- MAPKAPK3 p.Arg112His Uncertain significance ★★ ⚠ same type
- MAPKAPK3 p.Arg148Gln Uncertain significance ★★ ⚠ same type
- MAPKAPK3 p.Arg148Trp Uncertain significance ★★ ⚠ same type
- MAPKAPK3 p.Arg259Cys Uncertain significance ★★ same type
- MAPKAPK3 p.Arg282Cys Uncertain significance ★★ ⚠ same type
- MAPKAPK3 p.Arg282His Uncertain significance ★★ ⚠ same type
- MAPKAPK3 p.Arg319Gln 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/mapkapk3-p-thr40 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown