Identification of the TSC1 gene and neighbouring transcripts on human chromosome 9q34

Tuberous sclerosis is an inherited disease typically characterised by a facial rash, seizures and mental handicap. Patients suffer from benign tumours in many organs including the brain, heart, skin, kidneys, lungs and eyes. Genetic linkage studies show that the disease may be caused by a defect in one of two genes; TSC1 on chromosome 9q34 or TSC2 on chromosome 16p13. TSC2 had previously been identified and encodes a 180kD protein, tuberin, which may function as a GTPase activating protein (GAP). Previous genetic mapping studies delineated a candidate region for TSC1 of about 1.2Mb and physical mapping efforts had provided a complete cosmid contig of the region. This thesis describes exon trapping experiments performed in order to identify candidate genes in the region. Statistical analysis was subsequently performed in an attempt to determine why only a subset of exons were successfully trapped, but no significant factors were found. Exon trapping and EST mapping experiments in the candidate region allowed the identification and characterisation of several genes, including a gene which may encode a G protein subunit. Genomic sequence obtained from the cosmid contig as part of the Human Genome Project was analysed using a combination of database searching and gene prediction programs, resulting in the identification of several genes including one which appears to encode a sugar transporter. As part of a large collaborative effort, the TSC1 gene was identified. Its protein product, hamartin, has a coiled-coil domain but its function is unknown. Work described here includes mutation analysis of the gene and identification of neighbouring transcripts. The mutation screen in 79 tuberous sclerosis patients showed that most, if not all mutations in TSC1 are predicted to truncate the protein product prematurely, that TSC1 mutations are underrepresented in sporadic cases of tuberous sclerosis as compared to familial tuberous sclerosis, that non-penetrance is unlikely to exist in tuberous sclerosis and that a single ungual fibroma is not diagnostic of the disease