MAPK10 p.Lys116=
c.348G>A · rs1313496882 · VCV763905
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00334%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.323 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.088 | GERP -0.64, phastCons 0.52 |
| Overall | ||
| CADD | 9.966 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00334%
Admixed American · 2/59,878 alleles
Filtering AF
0.000554%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000207%
Overall
0.000434%
7/1,612,852 alleles · very rare
exomes 6/1,460,708 · genomes 1/152,144 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00334% | 29,939 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,416 |
| European (non-Finnish) | 0.000339% | 294,834 |
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
- MAPK10
- Protein
- p.Lys116=
- Coding
- c.348G>A
- MANE Select
- NM_138982
- dbSNP
- rs1313496882
- Type
- single nucleotide variant
- Location
- chr4:86107241 (GRCh38)
- Gene constraint
- LOEUF 0.54 · pLI 0.91 (gnomAD)
- Structure
- AlphaFold pLDDT 80.50 · 65 PDB
- Residue 116
- the protein kinase domain; a turn
Similar variants
- MAPK10 p.Ala320= Benign ★★ same type
- MAPK10 p.Asp351= Benign ★★ same type
- MAPK10 p.Val113= Benign/Likely benign ★★ same type
- MAPK10 p.Ala353Thr Uncertain significance ★ ⚠ same type
- MAPK10 p.Asn89Ser Uncertain significance ★ ⚠ same type
- MAPK10 p.Asp141Glu Uncertain significance ★ ⚠ same type
- MAPK10 p.Asp267Gly Uncertain significance ★ ⚠ same type
- MAPK10 p.Asp315Asn 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/mapk10-p-lys116 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown