Different SF3B1 Mutation Hotspots Show Hematopoietic Lineage-Specific VAF Patterns and Correlate with Distinct...

Background/Objectives: Myeloid neoplasms (MNs) with SF3B1 mutations define a distinct entity associated with a favorable prognosis. However, not all MN patients harboring SF3B1 mutations meet the diagnostic criteria for this entity, and different mutation types may be associated with distinct clinical outcomes. We aimed to evaluate the impact of variant allele frequency (VAF) and SF3B1 mutation type across hematopoietic lineages to improve patient stratification. Methods: VAF and the distribution of the p.K700E hotspot compared with other SF3B1 variants were evaluated using paired sequencing data from bone marrow (myeloid) and CD3⁺ (non-myeloid) samples from 23 MN patients with SF3B1 mutations to assess their association with clinical outcomes. Results: Overall, 47.8% of SF3B1 mutations detected in myeloid samples (VAF 42.4%) were also identified in the lymphoid lineage (VAF 17.8%). SF3B1 VAF in CD3⁺ samples correlated with worse prognosis markers. No differences were observed in overall co-mutation burden; however, only myeloid-restricted SF3B1 mutations appeared to represent initiating events. p.K700E mutations (n = 12) were restricted to the myeloid lineage, whereas non-p.K700E mutations (n = 11) were predominantly detected in both myeloid and lymphoid lineages, suggesting multilineage involvement. Conclusions: Distinct mutational patterns and clonal progression mechanisms were observed for different SF3B1 mutation types and depending on the affected hematopoietic lineage. Our findings suggest that the SF3B1 VAF across different lineages may refine patient stratification beyond mutation type alone.