RESUMO
Approximately half of gene lesions responsible for human inherited diseases are due to an amino acid substitution, showing that this mutational mechanism plays a large role in diseases. Distinguishing neutral sequence variations from those responsible for the phenotype is of major interest in human genetics. Because in vitro validation of mutations is not always possible in diagnostic settings, indirect arguments must be accumulated to define whether a missense variation is causative. To further differentiate neutral variants from pathogenic nucleotide substitutions, we developed a new tool, UMD-Predictor. This tool provides a combinatorial approach that associates the following data: localization within the protein, conservation, biochemical properties of the mutant and wild-type residues, and the potential impact of the variation on mRNA. To evaluate this new tool, we compared it to the SIFT, PolyPhen, and SNAP software, the BLOSUM62 and Yu's Biochemical Matrices. All tools were evaluated using variations from well-validated datasets extracted from four UMD-LSDB databases (UMD-FBN1, UMD-FBN2, UMD-TGFBR1, and UMD-TGFBR2) that contain all published mutations of the corresponding genes, that is, 1,945 mutations, among which 796 different substitutions corresponding to missense mutations. Our results show that the UMD-Predictor algorithm is the most efficient tool to predict pathogenic mutations in this context with a positive predictive value of 99.4%, a sensitivity of 95.4%, and a specificity of 92.2%. It can thus enhance the interpretation of variations in these genes, and could easily be applied to any other disease gene through the freely available UMD generic software (http://www.umd.be).
Assuntos
Substituição de Aminoácidos/genética , Biologia Computacional/métodos , Bases de Dados Genéticas , Proteínas dos Microfilamentos/genética , Nucleotídeos/genética , Receptores de Fatores de Crescimento Transformadores beta/genética , Software , Animais , Fibrilina-1 , Fibrilina-2 , Fibrilinas , Humanos , Mutação de Sentido Incorreto/genética , Proteínas Serina-Treonina Quinases/genética , Receptor do Fator de Crescimento Transformador beta Tipo I , Receptor do Fator de Crescimento Transformador beta Tipo IIRESUMO
Congenital contractural arachnodactyly (CCA) is an extremely rare disease, due to mutations in the FBN2 gene encoding fibrillin-2. Another member of the fibrillin family, the FBN1 gene, is involved in a broad phenotypic continuum of connective-tissue disorders including Marfan syndrome. Identifying not only what is in common but also what differentiates these two proteins should enable us to better comprehend their respective functions and better understand the multitude of diseases in which these two genes are involved. In 1995 we created a locus-specific database (LSDB) for FBN1 mutations with the Universal Mutation Database (UMD) tool. To facilitate comparison of identified mutations in these two genes and search for specific functional areas, we created an LSDB for the FBN2 gene: the UMD-FBN2 database. This database lists 26 published and six newly identified mutations that mainly comprise missense and splice-site mutations. Although the number of described FBN2 mutations was low, the frequency of joint dislocation was significantly higher with missense mutations when compared to splice site mutations.
Assuntos
Bases de Dados Genéticas , Proteínas dos Microfilamentos/genética , Mutação/genética , Análise Mutacional de DNA , Fibrilina-1 , Fibrilina-2 , Fibrilinas , Regulação da Expressão Gênica , Genótipo , Humanos , Proteínas dos Microfilamentos/metabolismo , Fenótipo , Polimorfismo Genético , Homologia de Sequência do Ácido NucleicoRESUMO
DYT1 dystonia are one of the exceptions in human genetics with its unique and recurrent mutation (c.907delGAG). In this rare movement disorder, the mutation is associated with incomplete penetrance as well as great clinical variability, making this disease a benchmark to search for genetic modifiers. Recently, Risch et al. have demonstrated the implication of the rs1801968 SNP in disease penetrance. We attempted to replicate this result in an exhaustive DYT1 French population with no success. Our results argue that the rs1801968 H allele effect is not part of the modifiers in the French population of DYT1 patients and that others have to be identified in our population.
Assuntos
Ácido Aspártico/genética , Distúrbios Distônicos/genética , Histidina/genética , Chaperonas Moleculares/genética , Polimorfismo de Nucleotídeo Único/genética , Alelos , Análise Mutacional de DNA , França/epidemiologia , França/etnologia , Frequência do Gene , HumanosRESUMO
The implication of mutations in the TGFBR2 gene, known to be involved in cancers, in Marfan syndrome (MFS) and later in Loeys-Dietz syndrome (LDS) and Familial Thoracic Aortic Aneurysms and Dissections (TAAD2) gives a new example of the complexity of one gene involved in multiple diseases. To date, known TGFBR2 mutations are not disease-specific and many mutations have to be accumulated before genotype-phenotype relationships emerge. To facilitate mutational analysis of the TGFBR2 gene, a locus-specific database has been set up with the Universal Mutation Database (UMD) software. The version of the computerized database contains 85 entries. A total of 12 mutations are reported to be involved in MFS, six in incomplete MFS, 30 in LDS type I, 10 in LDS type II, seven in TAAD2, and 20 in various cancers. The database is accessible online at http://www.umd.be (last accessed: 3 July 2007).