Browsing by Author "Almeida, L.S."
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- Characterization of novel SLC6A8 variants with the use of splice-site analysis tools and implementation of a newly developed LOVD databasePublication . Betsalel, O.T.; Rosenberg, E.H.; Almeida, L.S.; Kleefstra, T.; Schwartz, C.E.; Valayannopoulos, V.; Abdul-Rahman, O.; Poplawski, N.; Vilarinho, L.; Wolf, P.; den Dunnen, J.T.; Jakobs, C.; Salomons, G.S.The X-linked creatine transporter defect is caused by mutations in the SLC6A8 gene. Until now, 66 synonymous and intronic variants in SLC6A8 were detected in our laboratory. To gain more insight in the effect of the detected variants, we applied five free web-based splice-site analysis tools to 25 published variants that were stratified as (non-)disease causing. All were correctly predicted to have no effect (n¼18) or to cause erroneous splicing (n¼7), with the exception of a pathogenic de novo 24 bp intronic deletion. Second, 41 unclassified variants, including 28 novel, were subjected to analysis by these tools. At least four splice-site analysis tools predicted that three of the variants would affect splicing as the mutations disrupted the canonical splice site. Urinary creatine/creatinine and brain MRS confirmed creatine transporter deficiency in five patients (four families), including one female. Another variant was predicted to moderately affect splicing by all five tools. However, transient transfection of a minigene containing the variant in a partial SLC6A8 segment showed no splicing errors, and thus was finally classified as non-disease causing. This study shows that splice tools are useful for the characterization of the majority of variants, but also illustrates that the actual effect can be misclassified in rare occasions. Therefore, further laboratory studies should be considered before final conclusions on the disease-causing nature are drawn. To provide an accessible database, the 109 currently known SLC6A8 variants, including 35 novel ones, are included in a newly developed LOVD DNA variation database.
- "Double trouble” or digenic disorder in Complex I deficiencyPublication . Almeida, L.S.; Ferreira, M.; Nogueira, C.; Furtado, F.; Evangelista, T.; Santorelli, F.M.; Vilarinho, L.Complex I (CI) deficiency is a defect of OXPHOS caused by mutations in the mitochondrial or nuclear genomes. To date disease-causing mutations have been reported in all mitochondrial-encoded subunits and 22 nuclear genes. In about 50% of the patients no mutations are found, suggesting that undiscovered factors are an important cause of disease. In this study we report a consanguineous family from Southern Portugal with three affected children presenting with CI deficiency and 3-methylglutaconic aciduria type IV.
- Novel mutation in the mitochondrial transfer RNACys gene in a childPublication . Almeida, L.S.; Martins, E.; Santorelli, F.M.; Vilarinho, L.Mitochondrial DNA (mtDNA) disorders are an important group of genetic diseases presenting with a multifacet array of clinical manifestations. Highly energy-dependent tissues such as central nervous system and skeletal and cardiac muscles are commonly involved either as multisystem or as isolated organ disease. Characteristic symptoms include epilepsy, myopathy, deafness and ophthalmoplegia, all associated with point mutations in the mtDNA. Pathogenic mtDNA mutations can be heteroplasmic or homoplasmic. Heteroplasmic mutations are typically associated with mutations in mt-tRNA genes. Mutations in mt-tRNAs genes are responsible for the majority of the presentations of a mitochondrial disease being associated with marked clinical heterogeneity. Although tRNA-encoding genes make up only 9% of the entire mitochondrial genome, over 40% of all point mutations reported in the mtDNA are located in tRNA genes. Here, we present a child with vomiting episodes and migraine in whom we found a novel variant in the mitochondrial tRNACys gene.
- Nuclear-Mitochondrial Intergenomic Communication DisordersPublication . Almeida, L.S.; Nogueira, C.; Vilarinho, L.The focus of this chapter is to review the clinical and molecular etiologies of nuclear defects involved in mtDNA stability and in mitochondrial protein synthesis. The overview done here will hopefully provide insights towards best diagnostic strategies of mitochondrial cross–talk disorders, being useful for clinicians when facing similar cases. Additionally we will present a diagnostic algorithm for these diseases based on our knowledge.
- Relative frequency of known causes of multiple mtDNA deletions: two novel POLG mutationsPublication . Ferreira, M.; Evangelista, T.; Almeida, L.S.; Martins, J.; Macario, M.C.; Martins, E.; Moleirinho, A.; Azevedo, L.; Vilarinho, L.; Santorelli, F.M.Diseases affecting mtDNA stability, termed nuclear–mitochondrial intergenomic communication disorders, are caused by a primary nuclear gene defect resulting in multiple mtDNA deletions. The aim of this study was to estimate the frequency of known etiologies and the spectrum of mutations in a cohort of 21 patients harboring multiple mtDNA deletions in skeletal muscle. We showed that 10 cases (48%) display mutations in POLG, including eight previously reported variants and two novel mutations (namely, p.Trp585X and p.Arg1081Gln). The novel mutations affect evolutionary conserved residues and were absent in a large set of control chromosomes. These findings expand the array of mutations associated with multiple rearranged mtDNA attributed to mutations in POLG. The relatively high diagnostic yield (about one in two cases) supports the notion that it is recommended to test POLG routinely in diagnostic laboratories whenever multiple mtDNA deletions are present, regardless of the age of onset of patients and their clinical phenotype.
- Trimethylaminuria (fish odor syndrome): genotype characterization among Portuguese patientsPublication . Ferreira, F.; Esteves, S.; Almeida, L.S.; Gaspar, A.; da Costa CD, Janeiro P.; Bandeira, A.; Martins, E.S.; Teles, E.L.; Garcia, P.; Azevedo, L.; Vilarinho, L.Trimethylaminuria (TMAu) or "fish odor syndrome" is a metabolic disorder characterized by the inability to convert malodorous dietarily-derived trimethylamine (TMA) to odorless TMA N-oxide by the flavin-containing monooxygenase 3 (FMO3). Affected individuals unable to complete this reaction exude a "fishy" body odor due to the secretion of TMA in their corporal fluids leading to a variety of psychosocial problems. Interindividual variability in the expression of FMO3 gene may affect drug and foreign chemical metabolism in the liver and other tissues. Therefore, it is important to screen for common TMAu mutations but also extend the search to other genetic variants in order to correlate genotype and disease-associated phenotypes. In this study, 25 Portuguese patients with phenotype suggestive of TMAu were evaluated for molecular screening of the FMO3 gene. Herein, we found 16 variants in the FMO3 coding region, some of which had not been previously documented (Gly38Trp, Asp232Val, Thr307Pro, Ser310Leu). Whenever common variants (Glu158Lys, Glu308Gly) were considered in combination a distinct pattern between the control population and patients was observed, mainly in what concerns the presence of Lys158 and Gly308 in homozygous state. Further studies are necessary to clarify the pathogenicity of novel variants identified in this study, as well as the effect of the common single nucleotide polymorphisms, which may play an important role in disease presentation and/or protective mechanism to xenobiotics drugs or environment.