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Abstract
Human single nucleotide polymorphisms (SNPs) represent the most frequent type of human
population DNA variation. One of the main goals of SNP research is to understand the
genetics of the human phenotype variation and especially the genetic basis of human
complex diseases. Non-synonymous coding SNPs (nsSNPs) comprise a group of SNPs that,
together with SNPs in regulatory regions, are believed to have the highest impact
on phenotype. Here we present a World Wide Web server to predict the effect of an
nsSNP on protein structure and function. The prediction method enabled analysis of
the publicly available SNP database HGVbase, which gave rise to a dataset of nsSNPs
with predicted functionality. The dataset was further used to compare the effect of
various structural and functional characteristics of amino acid substitutions responsible
for phenotypic display of nsSNPs. We also studied the dependence of selective pressure
on the structural and functional properties of proteins. We found that in our dataset
the selection pressure against deleterious SNPs depends on the molecular function
of the protein, although it is insensitive to several other protein features considered.
The strongest selective pressure was detected for proteins involved in transcription
regulation.