Have a search on this site for SIFT and PolyPhen - these all predict effects of DNA mutations on protein function:
Here's your starter for 10
There is also the Variant Effect Predictor of Ensembl, which is offered as a web interface (for small numbers of variants) as well as a Perl API script:
Since you've added the protein tag I thought I'd link this:
It studies the structural & functional effects of a single protein point mutation fully automatically and displays a readable report with illustrations, which could be a nice start off point for further analysis. See also: "*Protein structure analysis of mutations causing inheritable diseases. An e-Science approach with life scientist friendly interfaces*"