Rationale:Tuberous sclerosis (TSC) is an autosomal dominant neurocutaneous syndrome resulting from mutations in the tumor suppressor genes TSC1 and TSC2. Unfortunately, the absence of accurate diagnosis has significantly impacted the well-being of both patients and their families. Furthermore, the pathogenicity of numerous variants remains unverified, which could potentially result in misinterpretation of their functional implications.Patient concerns:Proband 1 was a 33-year-old Chinese male, this patient presents with hamartomas in multiple organ systems, accompanied by clinical symptoms such as intellectual disability, epilepsy, and lipid adenoma. The patient and their family members used targeted next-generation sequencing and Sanger sequencing to identify the pathogenic variant.Diagnoses:The TSC1 (c.2923G>T, c.2924C>T) variant was identified and the patient was diagnosed with TSC disease.Interventions:After the definite diagnosis, the patient was treated with valproic acid, oxcarbazepine, and various organ supports.Outcomes:At present, the patient has intellectual decline, multiple sebaceous adenomas, multiple fiber nodules on the back, palpable mass in the right subcostal and middle upper abdomen, and percussion pain in the right kidney area, 1 to 2 times a month seizure, poor intelligence than peers.Lessons:This finding strengthens the significant phenotypic variability associated with TSC and expands the mutational spectrum of this rare disease.