There are online tools like SIFT, PANTHER, and PROVEAN that take snp inputs and then output whether that mutation will have an effect on the protein function.
I have several genome sequences with many mutations. Is there a way I can input for multiple proteins simultaneously?
Colleagues of mine here in Brno have a system that seems to work on VCF and other whole-genome data.
http://loschmidt.chemi.muni.cz/predictsnp2/
http://journals.plos.org/ploscompbiol/article?id=10.1371%2Fjournal.pcbi.1004962
Other than these, there is plenty of tools that allow batch queries. Suggested readings below.
https://www.ncbi.nlm.nih.gov/pubmed/25516408
https://www.ncbi.nlm.nih.gov/pubmed/?term=congruency+in+the+prediction+mazza
https://www.ncbi.nlm.nih.gov/pubmed/?term=A+Broad+Overview+of+Computational+Methods+for+Predicting+the+Pathophysiological+Effects+of+Non-synonymous+Variants
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