We then summarized the clinical characteristics of the AML patient (Pt. Song) harboring the novel NPM1 exon 5 mutation (NPM1_MutSong) (Additional file 1: Table S3). Besides NPM1 mutation, she also carried WT1 (VAF, 13.1%), IKZF1 (VAF, 17.8%), JAK2 (VAF, 4.6%), and NUP98 (VAF, 18.8%) mutations at the time of diagnosis. The patient was intravenously treated with daunorubicin 60 mg/m2 (days 1–3) plus cytarabine 100 mg/m2, intravenously (days 1–7) for induction, followed by 3 cycles of intermediate-dose cytarabine as consolidation. Then the patient received allogeneic hematopoietic stem cell transplantation (allo-HSCT). Unfortunately, Pt. Song died of severe pulmonary infection and viral encephalitis 14 months after the initial remission, 7 months after allo-HSCT.

The novel mutant exhibited several similar concomitant clinical features as type A mutation. Compared with commonly co-mutated genes such as DNMT3A and TET2, NPM1 mutations are generally presented at lower VAFs [11]. Since mutations acquired later in disease development exhibited lower VAFs than earlier mutations [12], the moderate VAFs suggest that NPM1 mutations may be a late event in leukemogenesis. In our patient, all the mutations showed moderate VAFs. Although our patient did not carry FLT3-ITD mutation, remarkably, she carried the WT1 mutation. While the classic NPM1 mutation alone is reportedly a favorable factor for AML with normal cytogenetics, sole WT1 mutation has been reported to be associated with poor prognosis [13]. Interestingly, data from a large cohort of AML patients showed that the coexistence of WT1 and NPM1 mutations significantly altered the positive prognostic impact of NPM1 mutations alone [13], underscoring the importance of more aggressive treatment for this subpopulation. Thus, our patient underwent allo-HSCT after initial remission, but unfortunately, ultimately died of severe pulmonary infection and viral encephalitis.

In this study, we reported a novel NPM1 mutation in exon 5 in a de novo AML patient, which resulted in cytoplasmic dislocation of NPM1 protein. Our findings strongly support that besides the exon 12 mutation, the exon 5 mutant is another NPM1 “born to be exported” mutant critical for leukemogenesis. Therefore, similar to the classic type A mutation, identification of our novel NPM1 mutation is beneficial for clinical laboratory diagnosis, genetic risk assessment and MRD monitoring.