Identification of a novel TSC1 gene variant in a patient with atypical vitiligo‐like skin lesions: Unveiling the hidden tuberous sclerosis complex

Background Tuberous sclerosis complex (TSC), an autosomal‐dominant disorder, is characterized by hamartomas affecting multiple organ systems. The underlying etiology of TSC is the pathogenic variations of the TSC1 or TSC2 genes. The phenotype variability of TSC could lead to missed diagnosis; therefore, the latest molecular diagnostic criteria for identifying a heterozygous pathogenic variant in either the TSC1 or TSC2 gene filled this gap. Furthermore, the pathogenicity of numerous variants remains unverified, potentially leading to misinterpretations of their functional consequences. Methods In this study, a single patient presenting with atypical vitiligo‐like skin lesions suspected to have TSC was enrolled. Targeted next‐generation sequencing and Sanger sequencing were employed to identify a pathogenic variant. Additionally, a minigene splicing assay was conducted to assess the impact of TSC1 c.1030‐2A>T, located in intron 10, on RNA splicing. Results A novel TSC1: c.1030‐2A>T heterozygosis variant was identified in intron 10. In vitro minigene assay revealed that the c.1030‐2A>T variant caused exon 11 skipping, resulting in a frameshift in the absence of 112 base pairs of mature messenger RNA and premature termination after 174 base pairs (p.Ala344Glnfs*59). Conclusion The detection of this novel pathogenic TSC1 variant in the patient with atypical vitiligo‐like skin lesions enrolled in our study ultimately resulted in the diagnosis of TSC. As a result, our study contributes to expanding the mutational spectrum of the TSC1 gene and refining the genotype–phenotype map of TSC. We revealed the impact of a novel TSC1 splicing variant on RNA splicing via a minigene assay, thus broadening the mutational spectrum of the TSC1 gene.