MAPK15 p.Arg56=
c.166A>C · VCV3293205
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00915%, nfe)
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 9 | GERP 1.6, phastCons 1 |
| Overall | ||
| CADD | 17.01 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00915%
European (non-Finnish) · 108/1,179,990 alleles
Filtering AF
0.00774%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00719%
Overall
0.00713%
115/1,613,950 alleles · very rare
exomes 106/1,461,838 · genomes 9/152,112 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00915% | 10,926 |
| Remaining individualsnot grpmax-eligible | 0.008% | 12,497 |
| African / African-American | 0.00267% | 37,444 |
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
- MAPK15
- Protein
- p.Arg56=
- Coding
- c.166A>C
- MANE Select
- NM_139021
- Type
- single nucleotide variant
- Location
- chr8:143718047 (GRCh38)
- Gene constraint
- LOEUF 1.344 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 69.56
- Residue 56
- the protein kinase domain
Similar variants
- MAPK15 p.Arg496Trp Uncertain significance ★★ ⚠ same type
- MAPK15 p.Ser192Ter Likely benign ★★ same type
- MAPK15 p.Ala179Thr Uncertain significance ★ ⚠ same type
- MAPK15 p.Ala251Val Uncertain significance ★ ⚠ same type
- MAPK15 p.Ala295Thr Uncertain significance ★ ⚠ same type
- MAPK15 p.Ala40Val Uncertain significance ★ ⚠ same type
- MAPK15 p.Ala436Ser Uncertain significance ★ ⚠ same type
- MAPK15 p.Ala436Val 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/mapk15-p-arg56 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown