MAPK10 p.Pro310=
c.930C>G · rs779714501 · VCV747293
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.02%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.09 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP 1.8 | GERP -1.8, phastCons 1 |
| Overall | ||
| CADD | 9.823 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.02%
Admixed American · 12/59,980 alleles
Filtering AF
0.0115%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00898%
Overall
0.000867%
14/1,613,862 alleles · ultra-rare
exomes 12/1,461,736 · genomes 2/152,126 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.02% | 4,998 |
| African / African-American | 0.00267% | 37,452 |
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.Pro310=
- Coding
- c.930C>G
- MANE Select
- NM_138982
- dbSNP
- rs779714501
- Type
- single nucleotide variant
- Location
- chr4:86067828 (GRCh38)
- Gene constraint
- LOEUF 0.54 · pLI 0.91 (gnomAD)
- Structure
- AlphaFold pLDDT 80.50 · 65 PDB
- Residue 310
- the protein kinase domain; an α-helix
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-pro310 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown