RATIONALE: Tuberous sclerosis complex is a multisystem genetic disorder caused by variant of TSC1 or TSC2, which were defined as an independent diagnostic criterion for TSC. PATIENT CONCERNS: We present a novel hereditary variant in a family. The family showed a phenomenon of familial aggregation in the Tuberous sclerosis complex. DIAGNOSES: The proband had the c.3974del (exon 33) (p.Gly1325Alafs*58) loss of heterozygosity frameshift in the TSC2 gene (chr16), which was 1 base deletion on the coding sequence of TSC2, leading to a frameshift mutation. Moreover, the novel variant occurred in the grandchildren (generation 3) also can be detected in the grandparental (generation 1) and parental (generation 2). INTERVENTIONS: The proband had taken antiepileptic drugs (oxcarbazepine [30 mg/(kg·day)], depakine [28 mg/(kg·day)], levetiracetam [38 mg/(kg·day)], and lamotrigine [2 mg/(kg·day)]) and performed a right parietal resection of the epileptic lesion. OUTCOMES: The treatment received by the proband was ineffective. LESSONS: The novel gene mutation sites to be found provide more research entry points for genetic diagnosis, providing new clinical data for tuberous sclerosis complex research.