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PAHdb Abstract

PAHdb: A locus-specific mutation knowledgebase focusing on their associations and effects

PAHdb is an online relational locus-specific database (http://www.pahdb.mcgill.ca) for mutations in the human phenylalanine hydroxylase gene (symbol PAH) and the associated phenotypes at the levels of protein, metabolites and organism. When combined with information about associations of mutations with populations, haplotypes and other features, PAHdb operates as a knowledge base. PAHdb is disease-oriented for hyperphenylalaninemia (HPA) (see OMIM 261600) due to primary deficiency of PAH enzyme function (EC 1.14.16.1). PAHdb and its numerous modules are, in practice, maintained by a team of curators who follow guidelines for nomenclature (Antonarakis et al. Hum Mutat 11:1-3, 1998; Human Gene Nomenclature Committee: http://www.gene.ucl.ac.uk/nomenclature), and for content, design and deployment (Scriver et al. Hum Mutat 13:344-350, 1999). PAHdb accepts and validates direct online submissions of mutation and auxiliary information. Content of PAHdb includes the cDNA sequence (GenBank U49897.1) and the genomic sequence (GenBank AF404777). All alleles have the appropriate context (species, locus, gene, unique identifier number, name and source of information); are identifiable by the SRS search engine and are recognizable as either pathogenic (phenotype modifying) or polymorphic (putatively neutral in effect). A platform for molecular modeling shows a crystal structure and amino acid residues at 2.0 resolution. Separate tables provide results of In Vitro Expression analysis; 57 naturally occurring human PAH alleles (109 records); 24 artificial rat PAH alleles (25 records); 6 artificial human alleles. Human genotype/phenotype correlations are available for a large number of mutations; raw data are stored in a repository accessible from the main page. Genetic models of HPA in the mouse are described in a separate module. Another module provides clinical information on HPA for patients and students, and about its treatment, with pointers to resources. A Curators' Page comments occasionally on relevant articles which cannot easily be deconstructed for entry into the database.

Copyright 2003 DeBelle Laboratory - Created [2002.10.17.208076] - Updated [2009.08.31]