MAPKAPK3 p.Val167=
c.501C>T · rs192866693 · VCV1078573
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0167%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.81 | GERP 0.29, phastCons 1 |
| Overall | ||
| CADD | 12.6 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0167%
Admixed American · 10/60,004 alleles
Filtering AF
0.009%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00681%
Overall
0.0013%
21/1,611,624 alleles · ultra-rare
exomes 11/1,459,528 · genomes 10/152,096 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0167% | 6,000 |
| East Asian | 0.00891% | 11,218 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,615 |
| South Asian | 0.0011% | 91,026 |
| European (non-Finnish) | 0.00017% | 589,626 |
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.Val167=
- Coding
- c.501C>T
- MANE Select
- NM_001243925
- dbSNP
- rs192866693
- Type
- single nucleotide variant
- Location
- chr3:50642329 (GRCh38)
- Gene constraint
- LOEUF 0.943 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 83.10 · 5 PDB
- Residue 167
- the protein kinase domain
Similar variants
- MAPKAPK3 p.Val167Ile Uncertain significance ★★ ⚠ same residue
- 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
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-val167 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown