A missense variant in Exon 9 of the ASNS gene causes splicing abnormality in an Infant with asparagine synthetase deficiency

Asparagine Synthetase Deficiency (ASNSD) is a rare neurodevelopmental disorder primarily caused by pathogenic homozygous or compound heterozygous variants in the ASNS gene. Clinical manifestations typically include microcephaly, severe psychomotor developmental delay, progressive encephalopathy, epilepsy, and other associated neurological abnormalities. Herein, we performed a comprehensive clinical assessment of a neonate presenting with microcephaly and hypotonia from a Chinese family. Whole-exome sequencing (WES) identified two novel compound heterozygous variants in the ASNS gene: c.1031-6_1041del (paternally inherited) and c.1049A>G (maternally inherited). The c.1031-6_1041del variant disrupts the canonical splice region and was classified as likely pathogenic. Notably, the c.1049A>G variant, localized to Exon 9, results in a missense substitution (p.Lys350Arg) and was predicted by in silico tools to induce aberrant splicing. Furthermore, functional validation via in vitro splicing assays confirmed that this missense variant leads to partial deletion of Exon 9, thereby possibly impairing the normal expression and function of the ASNS gene. These findings expand the mutational spectrum of ASNSD and provide critical insights into the pathogenic mechanisms underlying splicing dysregulation caused by missense variants in the ASNS gene.