Functional analysis of germline RUNX1 variants identified in individuals with suspected familial platelet disorder

Deleterious germline RUNX1 variants lead to familial platelet disorder with myeloid malignancies (FPDMM), an autosomal dominant disorder characterized by thrombocytopenia, qualitative platelet defects, and an increased risk of hematologic malignancies. Interpretation of variants of uncertain significance (VUSs) remains a major barrier to precision medicine for affected individuals and families, particularly because many RUNX1 variants are private. To address this challenge, we developed a comprehensive pipeline of well-established in vitro functional assays, including transactivation reporter assays, electrophoretic mobility shift assays, western blotting with cell fractionation, and immunofluorescence imaging to assess subcellular localization. We evaluated the functional impact of 26 RUNX1 VUSs identified in individuals referred to the NIH RUNX1 Natural History Study. Five established benign and six pathogenic variants were included as controls. Functional data were integrated with population allele frequencies, in silico predictions, and clinical phenotype and segregation data, enabling reclassification of 17 variants. Our findings also reveal key limitations of the current MM-VCEP variant interpretation guidelines, including overly stringent thresholds that exclude functionally impaired variants from classification. In addition, we demonstrate that the currently approved assays inadequately capture the pathogenic impact of C-terminal variants. These results underscore the importance of comprehensive functional data to support RUNX1 variant classification and inform clinical interpretation. Moreover, this work facilitates investigation of FPDMM pathogenesis and supports refinement of RUNX1-specific variant curation guidelines. We further advocate for development of additional functional assays, especially for variants affecting the RUNX1 C-terminus.