Sequence variations that affect gene function and cause phenotypic variation represent functional (also known as perfect or diagnostic) markers [ 59, 60].
INDEL occurring in functionally important regions of genes could affect gene function, through gene expression modification [ 61] or RNA structure alterations [ 62].
In silico predictions, as well as discordant segregation with EVA in an affected fraternal twin pair suggest that this sequence change may not actually affect gene function or expression [22], [23].
Mutations can affect gene function in several different ways.
Studies in budding yeast indicate that nuclear position can directly affect gene function.
We have been investigating the association between MI and SNPs that are located in genes and have the potential to affect gene function or expression.
A great amount of data has been accumulated on genetic variations in the human genome, but we still do not know much about how the genetic variations affect gene function.
Finally, although the SNPs in this study could potentially affect gene function, additional linkage disequilibrium analysis would be needed in order to determine if other SNPs in these region could better account for the associations with MI we observed.
It is possible that the variations in receptor signalling strength seen in the mammoth and Neanderthal MC1R gene analyses in vitro [1], [7] did not occur or affect gene function in their native organisms.
We conducted an analysis of 17,576 SNPs that could potentially affect gene function or expression in three case-control studies of MI and identified 5 SNPs in four genes (ENO1, FXN (2 SNPs), HLA-DPB2, and LPA) that were associated with MI.
Most of these SNPs (65%) could potentially affect gene function or expression because they cause an amino-acid change in a predicted open reading frame (missense SNPs), or they are located in exon acceptor or donor splice site, and could change the splicing pattern of predicted open reading frames.
