AbstractBackgroundMultiple sulfatase deficiency (MSD) (MIM#272200) is an ultra‐rare autosomal recessive lysosomal storage disorder caused by mutation of the Sulfatase Modifying Factor 1 (SUMF1) gene.MethodsHerein, we report an eight‐year‐old boy with a late infantile form of multiple sulfatase deficiency. A combination of copy‐number variation sequencing (CNV‐seq) and whole‐exome sequencing (WES) were used to analyze the genetic cause for the MSD patient.ResultsOur results, previously not seen in China, show a novel compound heterozygous mutation with one allele containing a 240.55 kb microdeletion on 3p26.1 encompassing the SETMAR gene and exons 4–9 of the SUMF1 gene, and the other allele containing a novel missense mutation of c.671G>A (p.Arg224Gln) in the SUMF1 gene. Both were inherited from the proband's unaffected parents, one from each. Bioinformatics analyses show the novel variation to be “likely pathogenic.” SWISS‐MODEL analysis shows that the missense mutation may alter the three‐dimensional (3D) structure.ConclusionsIn summary, this study reported a novel compound heterozygous with microdeletion in SUMF1 gene, which has not been reported in China. The complex clinical manifestations of MSD may delay diagnosis; however, molecular genetic analysis of the SUMF1 gene can be performed to help obtain an early diagnosis.