MAPK10 p.Val113=
c.339C>T · rs28760360 · VCV211434
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.88%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.088 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP 5.8 | GERP 2.1, phastCons 1 |
| Overall | ||
| CADD | 11.59 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.88%
African / African-American · 1,411/74,920 alleles
Filtering AF
1.8%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.77%
Overall
0.11%
1,773/1,613,020 alleles · low-frequency
exomes 958/1,460,830 · genomes 815/152,190 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.88% | 53 |
| Middle Eastern | 0.248% | 403 |
| Remaining individualsnot grpmax-eligible | 0.139% | 718 |
| Admixed American | 0.115% | 869 |
| European (non-Finnish) | 0.0159% | 6,307 |
| South Asian | 0.0044% | 22,751 |
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.Val113=
- Coding
- c.339C>T
- MANE Select
- NM_138982
- dbSNP
- rs28760360
- Type
- single nucleotide variant
- Location
- chr4:86107250 (GRCh38)
- Gene constraint
- LOEUF 0.54 · pLI 0.91 (gnomAD)
- Structure
- AlphaFold pLDDT 80.50 · 65 PDB
- Residue 113
- the protein kinase domain; an α-helix
Similar variants
- MAPK10 p.Ala320= Benign ★★ same type
- MAPK10 p.Asp351= 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
- MAPK10 p.Cys79Gly 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-val113 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown