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Background  Tuberous sclerosis complex (TSC) is an autosomal dominant disorder characterized by hamartomas in multiple organs associated with germline mutations in  TSC1  and  TSC2,  including exonic, intronic, or mosaic mutations. Gastrointestinal (GI) tract Lymphangioleiomyomatosis (LAM) is an extremely rare manifestation of TSC, with few reported cases. Herein, we aimed to determine the driver mutation, pathogenesis, and relationship of germline and somatic mutations of LAM through whole-genome sequencing (WGS) of the tumor and blood samples and whole transcriptome sequencing (WTS) analysis.    Case presentation  A nine-year-old girl with a full-blown TSC presented with abdominal masses detected during a routine check-up. Resected intestinal masses were diagnosed as LAM by thorough pathological examination. Interestingly, the LAM presented a somatic  TSC2  gene mutation in exon 24 (p.R905W, c.C2713T), and the patient had intron retention by a novel germline mutation in the intron region of  TSC2  (chr16:2126489, C > G).    Conclusion  Our case suggests that intron retention by a single nucleotide intronic mutation of  TSC2  is sufficient to develop severe manifestations of TSC, but the development of LAM requires an additional somatic oncogenic mutation of  TSC2 .    Supplementary Information  The online version contains supplementary material available at 10.1186/s13000-021-01138-8.

diagnostic pathology

A second hit somatic (p.R905W) and a novel germline intron-mutation of TSC2 gene is found in intestinal lymphangioleiomyomatosis: a case report with literature review