MSc (Med), Faculty of Health Sciences, University of the Witwatersrand / Mental retardation (MR) is estimated to affect ~2-3% of the general population and may result from genetic causes and/or environmental causes. X-linked mental retardation (XLMR) is a heterogeneous group of disorders with a broad range of phenotypes and can be classified into syndromic XLMR (S-XLMR) and nonsyndromic XLMR (NS-XLMR) types. A number of X-linked genes have been identified that are associated with the different forms of XLMR. In an attempt to refine the diagnostic service to patients with XLMR, the Division of Human Genetics, Molecular Laboratory at the National Health Laboratory Service (NHLS) has investigated a number of associated X-linked genes. The main objective of this project was to investigate three genes, FMR2, XNP and ARX, associated with NS-XLMR and their contribution to XLMR in the South African (SA) population of MR males. Patients from different ethnic groups, referred to the Division of Human Genetics for fragile X MR syndrome that tested negative for the FMR1 expansion mutation were investigated for mutations in these genes. In addition, a cohort of Black institutionalized males was also investigated. The FMR2 expansion mutation responsible for fragile X E syndrome was not identified in 1194 FMR1 expansion negative MR male patients. FMR2 allele distribution analysis showed that a GCC repeat size of 15 was common in the MR cohort, accounting for 42% of alleles identified. From a total of 210 FMR1 expansion negative MR male subjects screened for mutations in a hotspot region (exons 7, 8 and 9) of the XNP gene, none was found to have a mutation in this region. Two patients from a cohort of 868 FMR1 expansion negative MR males were found to have a mutation in the ARX gene – one patient tested positive for the common 24 bp duplication mutation and a second patient appeared to have a deletion in the region amplified. These results indicate that the FMR2, XNP and ARX genes do not contribute significantly to MR in the SA population. As a result of this study, routine DNA testing for the FMR2 expansion, mutation screening in the hotspot region of the XNP gene and screening for the common 24 bp duplication mutation in the ARX gene in FMR1 expansion negative MR male subjects will not be implemented. A retrospective analysis was also done on 1862 probands referred to the Molecular Genetics Diagnostic service from 1992 to 2009 for fragile X MR syndrome testing. The FMR1 full expansion mutation was detected in 6.2% of probands, higher than reported worldwide figures. FMR1 allele distribution analysis in a cohort of 1184 FMR1 expansion negative MR males showed that 29 CGG repeats was the most frequent repeat size observed, accounting for 32.6% of all alleles in the cohort. The analysis of FMR1 alleles in MR males shows a similar distribution between different ethnic groups and compares well with other reported studies. This study reinforces the presence of fragile X MR syndrome in the SA Black population. Molecular investigations were also undertaken on 3 patients clinically suspected to have X-linked -thalassaemia mental retardation syndrome (ATR-X) and extended family members. Mutations were identified in each of the patients – two patients were found to have a novel mutation in the XNP gene and the third patient had a common XNP mutation. As a result, carrier testing and prenatal diagnosis was made possible in these families. A large family positive for the FMR1 expansion causing fragile X A MR syndrome was investigated. As an incidental finding, 2 females were found to be compound heterozygotes for 2 FMR1 alleles. Extended family members were tested and their FMR1 status was determined. Haplotype analysis was used to track the high-risk X chromosome in the family. As a result of this investigation, females at risk for premature ovarian failure and fragile X tremor ataxia syndrome have been identified. The approach to testing genes implicated in NS-XLMR has to be refined to allow for a cheaper and more efficient alternative. The use of newer techniques such as CGH microarray and MLPA has allowed for better detection of mutations. Delineating the causes of MR and their molecular and cellular consequences will assist families but also provide insight into the mechanisms that are required for the normal development of cognitive functions in humans.