The Swiss-Prot variant page and the ModSNP database: a resource for sequence and structure information on human protein variants

Hum Mutat. 2004 May;23(5):464-70. doi: 10.1002/humu.20021.


Missense mutation leading to single amino acid polymorphism (SAP) is the type of mutation most frequently related to human diseases. The Swiss-Prot protein knowledgebase records information on such mutations in various sections of a protein entry, namely in the "feature," "comment," and "reference" fields. To facilitate users in obtaining the most relevant information about each human SAP recorded in the knowledgebase, the Swiss-Prot Variant web pages were created to provide a summary of available sequence information, as well as additional structural information on each variant. In particular, the ModSNP database was set up to store information related to SAPs and to manage the modeling of SAPs onto protein structures via an automatic homology modeling pipeline. Currently, among the 16,566 human SAPs recorded in the Swiss-Prot knowledgebase (release 42.5, 21 November 2003), more than 25% have corresponding 3D-models. Of these variants, 47% are related to disease, 26% are polymorphisms, and 27% are not yet clearly classified. The ModSNP database is updated and the subsequent model construction pipeline is launched with each weekly Swiss-Prot release. Thus, the ModSNP database represents a valuable resource for the structural analysis of protein variation. The Swiss-Prot variant pages are accessible from the NiceProt view of a Swiss-Prot entry on the ExPASy server (, via a hyperlink created for the stable and unique identifier FTId of each human SAP.

MeSH terms

  • Amino Acid Substitution*
  • Databases, Protein* / statistics & numerical data
  • Databases, Protein* / trends
  • Genetic Variation
  • Humans
  • Internet
  • Mutation, Missense*
  • Polymorphism, Genetic
  • Proteins / chemistry
  • Proteins / genetics
  • Sequence Analysis, Protein
  • Structural Homology, Protein*


  • Proteins