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We have identified polymorphic structural variants in a natural population and found evidence that many of these variants are deleterious.
In fact, assuming that all variants are deleterious works quite poorly, except for the step-up approach, which still did reasonably well.
However, they assume that all rare variants are deleterious; while this may be a reasonable assumption for many diseases [2], there is also the possibility that some rare variants are protective.
It is however well known that the predictions of which variants are deleterious or tolerated made by the latter are often not congruent with reality and should ideally be confirmed with in vitro or in vivo functional studies.
The two curves are not significantly different, and predict that as many as 28% of variants are deleterious (MutationTaster) or as few as 2% (MutationAssessor), with the two most commonly used algorithms, SIFT and PolyPhen2, giving intermediate estimates of 80% neutral.
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Our functional analysis of the A1708E TAD variant confirms our previous findings [ 3] that this variant is deleterious.
The SIFT and PolyPhen-2 protein function algorithms predicts this change to be tolerated and benign, whereas the MutationTaster program indicates that this c.13366C > T variant is deleterious.
In the nonsynonymous regions of these genes we compared the SIFT [13], PMUT [14], and PolyPhen [15] methods of predicting whether the variants were deleterious protein coding mutations.
A phylogenetic analysis of ancestral 'founding' variants could be used to investigate this hypothesis; if clearing variants were deleterious in the long term, then they would become extinct over short timescales.
Firstly, conventional protein functional prediction algorithms only provide a binary prediction on whether a variant is deleterious or tolerated.
Condel count: number of transcripts in which a given variant is deleterious; Condel max: maximal score from Condel; Condel algorithms: maximum number of algorithms (used in Condel score computation) in which a given variant is marked as deleterious.
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