title: A1ATVar: a relational database of human SERPINA1 gene variants leading to alpha1-antitrypsin deficiency and application of the VariVis software.
abstract: We have developed a relational database of human SERPINA1 gene mutations, leading to alpha(1)-antitrypsin (AAT) deficiency, called A(1)ATVar, which can be accessed over the World Wide Web at www.goldenhelix.org/A1ATVar. Extensive information has been extracted from the literature and converted into a searchable database, including genotype information, clinical phenotype, allelic frequencies for the commonest AAT variant alleles, methods of detection, and references. Mutation summaries are automatically displayed and user-generated queries can be formulated based on fields in the database. A separate module, linked to the FINDbase database for frequencies of inherited disorders allows the user to access allele frequency information for the three most frequent AAT alleles, namely PiM, PiS, and PiZ. The available experimental protocols to detect AAT variant alleles at the protein and DNA levels have been archived in a searchable format. A visualization tool, called VariVis, has been implemented to combine A(1)ATVar variant information with SERPINA1 sequence and annotation data. A direct data submission tool allows registered users to submit data on novel AAT variant alleles as well as experimental protocols to explore SERPINA1 genetic heterogeneity, via a password-protected interface. Database access is free of charge and there are no registration requirements for querying the data. The A(1)ATVar database is the only integrated database on the Internet offering summarized information on AAT allelic variants and could be useful not only for clinical diagnosis and research on AAT deficiency and the SERPINA1 gene, but could also serve as an example for an all-in-one solution for locus-specific database (LSDB) development and curation.
authors.affiliation: Medical Genetics Centre-Department of Cell Biology and Genetics, Faculty of Medicine and Health Sciences, Erasmus University Medical Center, Rotterdam, The Netherlands.
authors.forename: Sophia
authors.initials: S
authors.lastname: Zaimidou
authors.forename: Sjozef
authors.initials: S
authors.lastname: van Baal
authors.forename: Timothy D
authors.initials: TD
authors.lastname: Smith
authors.forename: Konstantinos
authors.initials: K
authors.lastname: Mitropoulos
authors.forename: Mila
authors.initials: M
authors.lastname: Ljujic
authors.forename: Dragica
authors.initials: D
authors.lastname: Radojkovic
authors.forename: Richard G
authors.initials: RG
authors.lastname: Cotton
authors.forename: George P
authors.initials: GP
authors.lastname: Patrinos
mesh_terms: D000483:Alleles; D001483:Base Sequence; D030541:Databases, Genetic; D005787:Gene Frequency; D014644:Genetic Variation; D005838:Genotype; D006801:Humans; D020407:Internet; D009154:Mutation; D010641:Phenotype; D012984:Software; D000515:alpha 1-Antitrypsin / Q000235:genetics*; D019896:alpha 1-Antitrypsin Deficiency / Q000235:genetics* / Q000473:pathology
chemical_list: C043392:SERPINA1 protein, human; D000515:alpha 1-Antitrypsin