MAP2K2 p.Lys172=
c.516A>G · rs886038699 · VCV261929
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.44 | donor gain · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.27 | GERP -3.9, phastCons 0.99 |
| Overall | ||
| CADD | 16.95 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- MAP2K2
- Protein
- p.Lys172=
- Coding
- c.516A>G
- MANE Select
- NM_030662
- dbSNP
- rs886038699
- Type
- single nucleotide variant
- Location
- chr19:4102388 (GRCh38)
- Gene constraint
- LOEUF 0.858 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.54 · 3 PDB
- Residue 172
- the protein kinase domain; an α-helix
Similar variants
- MAP2K2 p.Lys172Glu Uncertain significance ★★ ⚠ same residue
- MAP2K2 p.Lys172Arg Uncertain significance ★ ⚠ same residue
- MAP2K2 p.Glu207Lys Likely pathogenic ★★★ same type
- MAP2K2 p.Phe57Cys Pathogenic ★★★ same type
- MAP2K2 p.Phe57Val Pathogenic ★★★ same type
- MAP2K2 p.Pro128Gln Pathogenic ★★★ same type
- MAP2K2 p.Tyr134Cys Likely pathogenic ★★★ same type
- MAP2K2 p.Tyr134His Pathogenic ★★★ 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/map2k2-p-lys172 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown