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SNPeffect: a database mapping molecular phenotypic effects of human non-synonymous coding SNPs.

Joke Reumers1, Joost Schymkowitz, Jesper Ferkinghoff-Borg

  • 1SWITCH Laboratory, Flemish Interuniversity Institute for Biotechnology, Free University of Brussels, Pleinlaan 2, 1050 Brussels, Belgium.

Nucleic Acids Research
|December 21, 2004
PubMed
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SNPeffect is a new online database detailing the functional effects of human single nucleotide polymorphisms (SNPs) on protein molecular phenotypes. This resource aids genetic and biomedical research by linking allelic variation to protein attributes.

Area of Science:

  • Genomics
  • Proteomics
  • Bioinformatics

Background:

  • Single nucleotide polymorphisms (SNPs) are crucial in genetic and biomedical research.
  • Understanding the functional impact of SNPs on protein molecular phenotypes remains a challenge.

Purpose of the Study:

  • To develop SNPeffect, an online resource mapping phenotypic effects of human non-synonymous coding SNPs (nsSNPs).
  • To provide a comprehensive database for exploring how allelic variation affects protein function.

Main Methods:

  • Compilation of 31,659 nsSNPs from 12,480 human proteins.
  • Integration of data on protein stability, functional sites, post-translational modifications (phosphorylation, glycosylation), localization, turnover, aggregation, and chaperone interactions.
  • Development of search and browse interfaces with links to major biological databases.

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Main Results:

  • SNPeffect houses extensive data on the functional consequences of nsSNPs.
  • The resource links specific SNPs to changes in protein attributes like stability and localization.
  • Data is accessible for individual SNPs or aggregated per protein.

Conclusions:

  • SNPeffect serves as a valuable resource for understanding the molecular phenotype of human genetic variation.
  • The database facilitates research into the functional impact of nsSNPs in human genes.
  • SNPeffect will be regularly updated to incorporate new findings.