RUNX1 p.Ser424Pro

NM_001754.5(RUNX1):c.1270T>C (p.Ser424Pro) is a missense variant predicted to cause the substitution of serine by proline at amino acid 424 (p.S424P). This variant is absent from gnomAD v2, but in gnomAD v3, the highest population minor allele frequency is 0.07016% (4/4276 alleles) in the East Asian population, and in gnomAD v4, it is 2.641% (624/23626 alleles) in the East Asian population. Both frequencies are higher than the overall allele frequency of all disease-causing alleles derived by the ClinGen Myeloid Malignancy-VCEP. However, genomes failed a quality filter (AS_VQSR) in gnomAD v3 and v4, allele balance is heavily skewed, and site quality seems lower compared to some common, known pathogenic variants (BA1 not met). This variant has been reported in a 59-year-old female with thrombocytopenia and a secondary defect, who also carried RUNX1 c.1256T>G (p.Val419Gly) (phasing unclear) and a 2.5 Mb deletion including FLI1, although the germline origin was presumed rather than confirmed by tissue or familial testing (PMID: 32935436). Additionally, one individual in a Japanese family with B-ALL, likely due to PAX5 G183R, was found to carry this variant, while two siblings were negative (PMID: 35902733). Another patient reportedly with hereditary thrombocytopenia and hematological cancer predisposition associated with RUNX1 carried this variant in the germline, but an unspecified number of affected relatives in the family were negative (ClinVar Accession: SCV002515682.3). The variant has also been reported in patients with AML (PMID: 36900179), MDS (PMID: 36932114), and other tumors (PMID: 30239046; PMID: 30246500; PMID: 32943879; PMID: 35626111; PMID: 37160887; PMID: 37994105), though the variant allele fraction mostly suggests somatic origin or artifact (unconfirmed). No relevant functional data are available for this specific missense variant, but in vitro studies have demonstrated that Ser424 is a phosphorylation target of CDK/Cyclin complexes (PMID: 18003885). The computational predictor REVEL gives a score of 0.465, which is below the threshold of 0.50, and the splice site predictor SpliceAI indicates that the variant has no impact on splicing, suggesting it does not predict a damaging effect on RUNX1 function (BP4). In summary, this variant meets the criteria to be classified as a variant of uncertain significance (VUS) for autosomal dominant hereditary thrombocytopenia and hematologic cancer predisposition syndrome. ACMG/AMP criteria applied, as specified by the ClinGen Myeloid Malignancy VCEP: BP4.