MAP2K1 p.Pro124Ser

The NM_002755.4:c.370C>T variant in MAP2K1 is a missense variant predicted to cause substitution of proline by serine at amino acid 124 (p.Pro124Ser). This variant was absent from gnomAD v2.1.1 (PM2_Supporting). The computational prediction tool REVEL gives a score of 0.855, suggesting that this variant may impact the protein (PP3). The p.Pro124Ser variant is located in the MAP2K1 gene, which has been defined by the ClinGen RASopathy Expert Panel as a gene with a low rate of benign missense variants and pathogenic missense variants are common (PP2). The variant is in a location that has been defined by the ClinGen RASopathy Expert Panel to be a critical domain of MAP2K1 (AA 124-134, PM1). Furthermore, 4 different (likely) pathogenic variants at this residue (Pro124Leu, Pro124Arg, Pro124Ala, Pro124Gln) have been identified in several patients with RASopathies (PM5). This variant has been observed in at least 7 probands with a RASopathy, of which 3 were reported as a de novo occurrence with confirmed parental relationships and 1 was assumed to be de novo (PS2_VeryStrong, PS4_Moderate; PMIDs: 36777711, 32978145, GeneDx, LabCorp, ClinVar SCV000572401.6, SCV003316958.3). In vitro functional studies showed that the p.Pro124Ser variant led to ERK1/2 phosphorylation indicating that the mutant was constitutively active (PS3_Supporting; PMID: 22197931). In summary, this variant meets criteria to be classified as pathogenic for autosomal dominant RASopathy based on the ACMG/AMP criteria applied, as specified by the ClinGen RASopathy Variant Curation Expert Panel: PS2_VeryStrong, PS4_Moderate, PM1, PM5, PS3_Supporting PM2_Supporting, PP2, PP3 (Specification Version 2.3, 1/10/2025)