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PolyPhen-2 calculates a Naive Bayes posterior probability that any mutation is damaging by the representation of a score ranging from 0 to 1 and predicts qualitative damage based on the model's false positive rate (benign, possibly damaging, or probably damaging).
Protein modeling demonstrated that the missense mutation is damaging and may alter binding to ATP molecules.
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According to Alexey Kondrashov of the University of Michigan, an expert on the matter who wrote an article in Nature to accompany Dr Stefansson's study, about 10% of mutations are damaging.
Within the prioritized variants, those harboring truncating mutations or mutations predicted to be damaging were considered to be the most promising candidates.
In many types of cancer cells, the p53 gene is damaged by mutation.
Alternatively, it can be seen as an important factor of evolution, which, for example, provides a backup metabolism on which an organism can rely if the pathway that is currently important is damaged by mutation.
But when BRCA1 is damaged by a mutation, the signal to slow down is never relayed, and cell division can go on and on unchecked, leading to cancer.
Both mutations were predicted to be damaging by the CADD algorithm, and one mutation (p.Asp27His) was predicted to be damaging by SIFT algorithm (Ng and Henikoff, 2001; Kircher et al., 2014).
These three missense mutations were predicted to be damaging in functional prediction by SIFT and PolyPhen2.
Considering that about half of missense mutations are expected to be damaging to a typical protein [ 20], we expect that even a small allelic series will be useful for phenotypic analysis.
The amino acid change is not tolerated according to SIFT software and Polyphen predicts this mutation is probably damaging with a score at 1.868.
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