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On-line mutation prediction tools have been available for many years.
Novel LDLR variants were assessed by in silico mutation prediction tools, including PolyPhen2, SIFT, and Mutation Taster.
Ranking this subset of variants based on consequence (e.g., stop gains would rank higher than missense) and scores derived from mutation prediction tools (e.g., "probably damaging" variants would rank higher than "possibly damaging" according to Polyphen-2 prediction) would enable assessment of the predicted impact of all rare mutations.
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To assess the pathogenic role of these mutations, prediction tools are limited, in that they can only estimate the potential impact of a specific variation.
This mutation has not been reported before, but segregates with disease in this family, and is predicted to be "deleterious" and "possibly damaging" by two mutation effect prediction tools [ 34, 35].
However, it's unclear that this missense mutation is causal as the prediction tools are not conclusive (see Table 4).
In addition, the potential clinical relevance of novel variants with a predicted damaging effect (based on in silico prediction tools and type of mutation) was also assessed.
The computational biologists can utilize the compiled data to develop computational prediction tools for novel mutations.
Similar result calling for use of several tools was apparent when splice site prediction tools were tested for mutation analysis [ 18].
Comparison of this recent PSAAP algorithm with established on-line prediction tools may improve our understanding of predicting mutation status in the RET proto-oncogene.
All other genes were predicted by all three prediction tools.
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