Using single‐cell proteogenomic sequencing (ScPGseq), we attempted to identify a relapse‐fated subclone in an AML case with mutations in WT1, NPM1, and FLT3 tyrosine kinase domain and two FLT3‐ITDs (21 bp and 39 bp) (low AR) at presentation, then relapsed only with WT1 and NPM1 mutations and one FLT3‐ITD (high AR). The gene discussed is FLT3; the disease is acute myeloid leukemia.