Annotating single amino acid polymorphisms in the UniProt/Swiss-Prot knowledgebase

Abstract

UniProtKB/Swiss-Prot (http://beta.uniprot.org/uniprot; last accessed: 19 October 2007) is a manually curated knowledgebase providing information on protein sequences and functional annotation. It is part of the Universal Protein Resource (UniProt). The knowledgebase currently records a total of 32,282 single amino acid polymorphisms (SAPs) touching 6,086 human proteins (Release 53.2, 26 June 2007). Nearly all SAPs are derived from literature reports using strict inclusion criteria. For each SAP, the knowledgebase provides, apart from the position of the mutation and the resulting change in amino acid, information on the effects of SAPs on protein structure and function, as well as their potential involvement in diseases. Presently, there are 16,043 disease-related SAPs, 14,266 polymorphisms, and 1,973 unclassified variants recorded in UniProtKB/Swiss-Prot. Relevant information on SAPs can be found in various sections of a UniProtKB/Swiss-Prot entry. In addition to these, cross-references to human disease databases as well as other gene-specific databases, are being added regularly. In 2003, the Swiss-Prot variant pages were created to provide a concise view of the information related to the SAPs recorded in the knowledgebase. When compared to the information on missense variants listed in other mutation databases, UniProtKB/Swiss-Prot further records information on direct protein sequencing and characterization including posttranslational modifications (PTMs). The direct links to the Online Mendelian Inheritance in Man (OMIM) database entries further enhance the integration of phenotype information with data at protein level. In this regard, SAP information in UniProtKB/Swiss-Prot complements nicely those existing in genomic and phenotypic databases, and is valuable for the understanding of SAPs and diseases.