MAP2K1 p.Ile204=
c.612C>A · rs2140667598 · VCV1677018
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.094 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP 3.2 | GERP 0.15, phastCons 1 |
| Overall | ||
| CADD | 11.96 | 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
- MAP2K1
- Protein
- p.Ile204=
- Coding
- c.612C>A
- MANE Select
- NM_002755
- dbSNP
- rs2140667598
- Type
- single nucleotide variant
- Location
- chr15:66481798 (GRCh38)
- Gene constraint
- LOEUF 0.515 · pLI 0.97 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 84.05 · 99 PDB
- Residue 204
- the protein kinase domain; a β-strand
Similar variants
- MAP2K1 p.Ile204Met Uncertain significance ★ ⚠ same residue
- MAP2K1 p.Arg108Leu Likely pathogenic ★★★ same type
- MAP2K1 p.Asn122Asp Pathogenic ★★★ ⚠ same type
- MAP2K1 p.Asp67Asn Pathogenic ★★★ same type
- MAP2K1 p.Glu203Gly Pathogenic ★★★ same type
- MAP2K1 p.Leu42Arg Likely pathogenic ★★★ same type
- MAP2K1 p.Leu42Phe Pathogenic ★★★ same type
- MAP2K1 p.Leu92Arg 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/map2k1-p-ile204 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown