MAP3K11 p.Pro840=
c.2520G>A · VCV3870142
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00207%, 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 -10 | GERP -4.7 |
| Overall | ||
| CADD | 0.028 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00207%
European (non-Finnish) · 23/1,112,854 alleles
Filtering AF
0.00138%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00115%
Overall
0.00169%
25/1,477,434 alleles · very rare
exomes 21/1,325,168 · genomes 4/152,266 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00207% | 48,385 |
| Remaining individualsnot grpmax-eligible | 0.00178% | 56,046 |
| African / African-American | 0.00142% | 70,404 |
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
- MAP3K11
- Protein
- p.Pro840=
- Coding
- c.2520G>A
- MANE Select
- NM_002419
- Type
- single nucleotide variant
- Location
- chr11:65598315 (GRCh38)
- Gene constraint
- LOEUF 0.79 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 63.79 · 4 PDB
- Residue 840
- the 'disordered' region
Similar variants
- MAP3K11 p.Ala169Thr Uncertain significance ★ ⚠ same type
- MAP3K11 p.Ala282Pro Uncertain significance ★ ⚠ same type
- MAP3K11 p.Ala287Thr Uncertain significance ★ ⚠ same type
- MAP3K11 p.Ala352Ser Uncertain significance ★ ⚠ same type
- MAP3K11 p.Ala370Val Uncertain significance ★ ⚠ same type
- MAP3K11 p.Ala378Thr Uncertain significance ★ ⚠ same type
- MAP3K11 p.Ala39Gly Uncertain significance ★ ⚠ same type
- MAP3K11 p.Ala42Ser 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/map3k11-p-pro840 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown