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Acute promyelocytic leukemia (APL) is a kind of acute myeloid leukemia, which was characterized by the presence of PML/RARα fusion gene. Mutations in CHST3 have been previously reported to be associated with a rare phenotype of skeleton dysplasia, known as Spondyloepiphyseal dysplasia. Here we reported 1 patient with APL with CHST3 mutations.An 18-year-old girl was referred to the Hematology Department because of a lasting history (10 days) of repeated fever and bleeding on skin. The girl was of short stature for age and with short fingers. Double nail beds were short with anti-nail deformity.She was diagnosed with APL according to the 2016 WHO classification after a MICM analysis (bone marrow morphology [M], immunophenotype [I], cytogenetics [C], and molecular biology [M]). Whole exome sequencing revealed complex heterozygous mutations on CHST3. Further confirmation showed that 1 mutation (c.155T>G; p.Leu52Arg) was from her father and the other mutation (c.1414G>A; p.Glu472Lys) was from her mother.The patient received Idarubicin (8 mg/m2) injection intravenous drip for 3 days based on all-trans retinoic acid and arsenic trioxide induction therapy.The patient died from disseminated intravascular coagulation and multiple organ hemorrhage at 9 days after diagnosis.This case describes a patient with APL with complex heterozygous mutations on CHST3. Carbohydrate sulfotransferases were found to play an important role in metastatic spread of tumor cells. Whether the mutation status of CHST3 gene has relationship with APL pathogenesis and prognosis is unknown.