Abstract:

We report a child with the very long chain acyl-CoA dehydrogenase deficiency (VLCADD) caused by compound heterozygous variants in the ACADVL gene. The tandem mass spectrometry detection of the patient's blood showed the increased levels of multiple long-chain acylcarnitines, suggesting a potential disorder of long-chain or very long-chain fatty acid oxidation. Trio whole exome sequencing was performed, and candidate pathogenic variants were verified by Sanger sequencing. The child was found to carry the compound heterozygous variants in the ACADVL gene: c.623-3C>G and c.1366C>T(p.Arg456Cys), which were inherited from her mother and father with normal phenotypes. According to the American College of Medical Genetics and Genomics guidelines, the c.623-3C>G variant was initially classified as a variant of uncertain significance (PM2_Supporting+PM3+PP3+PP4), while the c.1366C>T(p.Arg456Cys) variant was classified as likely pathogenic (PM1+PM2_Supporting+PM3_Strong+PP1+PP3). To further clarify the etiology, minigene assays confirmed that the c.623-3C>G variant may affect alternative splicing through an exon-skipping mechanism, based on which this variant was upgraded to a likely pathogenic variant (PS3+PM2_Supporting+PM3+PP3+PP4). This study confirms that the compound heterozygous variants in the ACADVL gene are the causative factors for the proband in this pedigree, thereby expanding the variant and phenotypic spectrum of the ACADVL gene. It also demonstrates that the minigene assay can effectively validate the pathogenicity of splice site variants, providing a reliable basis for the precise interpretation of the variants with uncertain significance.

Key words: Very long chain acyl-CoA dehydrogenase deficiency, Muscular diseases, Acyl-CoA dehydrogenase, long-chain, ACADVL gene, Whole exome sequencing, RNA splice sites