RNA sequencing reveals a complete picture of a homozygous missense variant in a patient with VPS13D movement disorder: a case report and review of the literature

• Published in: Molecular genetics and genomics : MGG 2023-09, Vol.298 (5), p.1185-1199
• Main Authors: Baker, Elizabeth K., Han, Jingfen, Langley, William A., Reott, Michael A., Hallinan, Barbara E., Hopkin, Robert J., Zhang, Wenying
• Format: Article
• Language: English
• Subjects: Animal Genetics and Genomics; Aversion; Biochemistry; Biomedical and Life Sciences; Case reports; Exome Sequencing; Genomes; Human Genetics; Humans; Infant; Life Sciences; Literature reviews; Male; Microbial Genetics and Genomics; Movement Disorders; mRNA turnover; Mutation; Neurological diseases; Nonsense-mediated mRNA decay; Original Article; Paralysis; Pathogenicity; Plant Genetics and Genomics; Proteins; RNA; Seizures; Sequence Analysis, RNA; Splicing
• ISSN: 1617-4615; 1617-4623
• DOI: 10.1007/s00438-023-02044-y

RNA sequencing (RNA-seq) is a complementary diagnostic tool to exome sequencing (ES), only recently clinically available to undiagnosed patients post-ES, that provides functional information on variants of unknown significance (VUS) by evaluating its effect on RNA transcription. ES became clinically available in the early 2010s and promised an agnostic platform for patients with a neurological disease, especially for those who believed to have a genetic etiology. However, the massive data generated by ES pose challenges in variant interpretation, especially for rare missense, synonymous, and deep intronic variants that may have a splicing effect. Without functional study and/or family segregation analysis, these rare variants would be likely interpreted as VUS which is difficult for clinicians to use in clinical care. Clinicians are able to assess the VUS for phenotypic overlap, but this additional information alone is usually not enough to re-classify a variant. Here, we report a case of a 14-month-old male who presented to clinic with a history of seizures, nystagmus, cerebral palsy, oral aversion, global developmental delay, and poor weight gain requiring gastric tube placement. ES revealed a previously unreported homozygous missense VUS, c.7406A > G p.(Asn2469Ser), in VPS13D . This variant has not been previously reported in genome aggregation database (gnomAD), ClinVar, or in any peer-reviewed published literature. By RNA-seq, we demonstrated that this variant mainly impacts splicing and results in a frameshift and early termination. It is expected to generate either a truncated protein, p.(Val2468fs*19), or no protein from this transcript due to nonsense-mediated mRNA decay leading to VPS13D deficiency. To our knowledge, this is the first case utilizing RNA-seq to further functionally characterize a homozygous novel missense VUS in VPS13D and confirm its impact on splicing. This confirmed pathogenicity gave the diagnosis of VPS13D movement disorder to this patient. Therefore, clinicians should consider utilizing RNA-seq to clarify VUS by evaluating its effect on RNA transcription.