The proportion of mutations predicted to have a deleterious effect differs between gain and loss of function genes in neurodegenerative disease

As more studies are turning to bioinformatic prediction programs to assess the potential impact of amino acid substitutions, it is relevant to evaluate the prediction results these programs give in genes that have been well-characterized for Mendelian diseases. Eight genes responsible for neurodegenerative disease with many identified mutations were sub-grouped into those that either have a gain or loss of function disease mechanism. Three prediction programs, PolyPhen, Panther and SIFT, were queried for the reported missense mutations. The mean percent of benign mutations was significantly higher in gain of function genes using the PolyPhen program (38% versus 21%, p=0.007). The probability that a gain of function mutation was predicted to have a damaging role was also significantly less using the Panther program (p=4.86x10(-12)). In contrast, there was no difference between gain and loss of function gene when the SIFT program was used. However, the most accurate distinction between gain and loss of function genes could be obtained when considering the mutations for which all three programs predicted the same result. Further, stratification of SOD1 mutations indicated that only the PolyPhen program could distinguish mutations that impaired enzymatic activity of SOD1 from those with near wildtype activity. The profile of benign and damaging changes from these genes will aid in the interpretation of bioinformatic prediction program results from missense mutations identified in novel genes.