The detection of 8 intronic and synonymous variants causative of splicing alterations in ATP7B led to the definitive diagnosis of 8 patients with suspected Wilson disease, according to a recently published study in the Journal of Molecular Diagnostics.

Wilson disease is a clinically heterogeneous disease with symptoms ranging from neuropsychiatric manifestations to liver failure and nephritis. This vast array of clinical presentations can make it difficult to achieve a diagnosis, thus preventing early treatment administration. Furthermore, several guidelines require the detection of pathogenic ATP7B variants to confirm the diagnosis.

Although next-generation sequencing (NGS) has increased the number of identified ATP7B pathogenic variants, there is a significant proportion of patients with suspected Wilson disease in whom no pathogenic variants are detected. 

Read more about Wilson disease etiology

Therefore, the authors aimed to analyze the NGS screening results of 12 patients with suspected Wilson disease to detect intronic and synonymous ATP7B variants of pathogenic significance, identifying 14 potentially pathogenic variants.

Of the 12 patients included in the study, 4 presented with neuropsychiatric manifestations, 4 presented with liver function abnormalities, and 4 had significant corneal Kayser-Fleischer rings. All patients had low ceruloplasmin levels.

After in silico splicing analysis, 5 of the initially identified variants were not associated with any significant splicing alterations, leaving 4 intronic variants and 4 synonymous variants with potential pathogenic significance. 

Minigene system validation revealed that these variants could lead to splicing alterations in the corresponding exon regions. In vivo reverse transcription-polymerase chain reaction analysis verified the previously described findings. 

The reinterpretation of the American College of Medical Genetics and Genomics pathogenicity of the 8 variants associated with ATP7B splicing changes by minigene system validation led to the confirmation of Wilson disease in 8 of the 12 patients included in the study. 

“Research on inherited rare diseases needs to revisit the significance of synonymous or intronic variants, and elucidating the pathogenicity of these variants through splicing functional experiments could help further improve genetic diagnosis, avoid delayed treatment, and possibly provide future directions for gene therapy,” the authors concluded.

Reference

Xu WQ, Wang RM, Dong Y, Wu ZY. Pathogenicity of intronic and synonymous variants of ATP7B in Wilson diseaseJ Mol Diagn. Published online January 1, 2023. doi:10.1016/j.jmoldx.2022.10.002