A 2-bp deletion mutation in SMPD1 gene leading to lysosomal acid sphingomyelinase deficiency in a Chinese consanguineous pedigree

Background Niemann-Pick disease type A (NPDA, MIM: 257200) is an autosomal recessive sphingolipidosis caused by lysosomal acid sphingomyelinase (ASM) deficiency. A cluster of genes located at chromosome 11p15 have been reported to be imprinted genes, such as TSSC5, TSSC3, and ZNF215 that flanking SMPD1 gene. It was reported by a few recent studies that SMPD1 gene was paternally imprinted and maternally preferentially expressed. Case presentation A five-month-old boy with severe anemia, hepatosplenomegly and bone marrow foam cells was recruited from a complete cousin couple. To determine whether boy suffered from NPDA, ASM activity and SMPD1 gene sequencing were performed on available individuals of this pedigree including the proband, his parents and sister. The ASM activities of proband and parents showed deficiency (17.7 nmol/h/g-protein) and about 50% decreased (83.3 nmol/h/g-protein), respectively, compared with normal controls (204.5 nmol/h/g-protein). SMPD1 gene sequencing in the proband revealed a homozygous mutation c.1420_1421del, which leads to an open reading frameshift and a premature stop codon. The parents and some individuals of this family demonstrated heterozygous mutation at this locus. To investigate whether SMPD1 gene is imprinted as reported previously, the expression of RNA level was studied in the whole family members available. The members with heterozygous mutation for c.1420_1421del showed that both paternal and maternal inherited alleles were expressed. Conclusions This study reported a c.1420_1421del mutation in SMPD1 gene which caused ASM activity decrease and this locus was biallelically expressed in heterozygous subjects implicating SMPD1 is not imprinted in this family.