J. R. Gilbert (Y) 7 V. Guy 7 M. A. Pericak-Vance Center for Human Genetics, Duke University Medical Center, Durham, North Carolina, USA C. Wolpert 7 M. A. Pericak-Vance Section of Medical Genetics, Duke University Medical Center, Durham, North Carolina, USA J. R. Gilbert 7 A. D. Roses Division of Neurology, Duke University Medical Center, Durham, North Carolina, USA A. Kumar Case-Western Reserve University School of Medicine, Cleveland, Ohio, USA R. Kandt Bowman Gray School of Medicine, Winston-Salem, North Carolina, USA A. Aylesworth University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA Neurogenetics (1998) 1 : 267–272 Q Springer-Verlag 1998 Original article Mutation and polymorphism analysis in the tuberous sclerosis 2 (TSC2 ) gene J. R. Gilbert 7 V. Guy 7 A. Kumar 7 C. Wolpert 7 R. Kandt 7 A. Aylesworth 7 A. D. Roses M. A. Pericak-Vance Received: December 29, 1997 / Accepted: March 24, 1998 ABSTRACT Tuberous sclerosis complex (TSC) is an autosomal dominant multi-system disorder with two known dis- ease loci on chromosomes 9q34 (TSC1) and 16p13.3 (TSC2). TSC has a prevalence of approximately 1 in 5,000–6,000, exhibits incomplete penetrance, and oc- curs in all racial groups. Our laboratory has undertaken the complete mutation analysis of the TSC2 gene in 42 TSC families using single-strand conformation poly- morphism analysis and reverse transcription-polymer- ase chain reaction. Of the total of 42 families, 16 show evidence of linkage to the chromosome 16 TSC2 locus and 26 are either sporadic or too small to establish chromosome linkage. The TSC2 gene spans at least 45 kilobases of genomic DNA, has 41 known exons, and codes for a 5,474-base pair transcript. After complete gene analysis, 16 TSC2 mutations have been identified, including DNA insertions, deletions, splice site muta- tions, and amino acid substitutions. The majority of pu- tative TSC2 mutations were found in sporadic rather than TSC2-linked families. We have also detected 15 polymorphisms which occur in the TSC2 gene. Key words TSC2 7 Mutation/polymorphism 7 Analysis INTRODUCTION Tuberous sclerosis complex (TSC) is an autosomal dominant disorder that affects numerous organs, espe- cially the brain, kidneys, heart, and skin. TSC is charac- terized by hamartomas (benign overgrowths predomi- nantly of a cell or tissue type that occurs normally in the organ) and hamartias (developmental abnormali- ties of tissue combination). Clinical symptoms can range from benign hypopigmented macules of the skin to profound mental retardation with intractable sei- zures to premature death from a variety of disease-as- sociated causes. The estimated prevalence of TSC is 1 in 5,000–6,000, it occurs in all racial groups, and two- thirds of new cases are believed to be the result of new mutations. Genetic studies have linked TSC to two loci on 9q34 (TSC1) [1] and 16p13 (TSC2) [2]. The TSC1 gene has 23 exons and an mRNA transcript of approximately 8,600 base pairs (bp), which contains a 3,492-bp open reading frame that codes for a 1,164-amino acid protein [3]. The protein, which has been named hamartin, is widely expressed and is believed to act as a tumor sup- pressor. The TSC2 gene, which was isolated in 1993, is expressed widely in different tissues, has at least 41 ex- ons covering a minimum of 45 kilobases (kb), and codes for an approximately 5,474-bp mRNA transcript [4, 5]. The expressed product of this gene, named tuber- in, codes for a 1,784-amino acid protein which shows stretches of homology to the GTPase activating protein GAP3. Loss of heterozygosity studies indicate that sec- ond somatic mutations are necessary at the cellular lev- el for phenotypic expression and are consistent with the TSC2 gene functioning as a tumor suppressor gene [6].