this is a good question. there are many other tools to investigate the functional effect of the SNPs.
in first istance you can model the SNPs into your protein structure of interest simple using the homology modeling (using mutate_model that you can get from the website of modeller) once you obtain yuor structure with the point mutation yuo can perform three type of analysis using three bioinformatics tools :
DSSP you can assigne secondary structure both wildtype and to the variant protein and than you compare if there are a differences in the secondary structure(note that DSSP do not predict the secondary structure but only assigne a possibile structure)
HBPLUS you can use this tool to perform the analysis of the hydrogen bond to evaluate the pattern of hydrogen bond
NACCESS you can use this tools to evalute the accessible areas of the molecule
if you have any questions can contact me