We are updating SIFT and PolyPhen-2 predictions of missense variant deleteriousness in the Ensembl browser and Ensembl VEP with the new release 109. We have recalculated all scores using newer software versions, updating PolyPhen-2 from 2.2.2 to 2.2.3 and SIFT from version 5.2.2 to 6.2.1. When we update software and reference data versions, we expect to see changes in some predictions. This is a guide as to what you can expect.
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Cool stuff the Ensembl VEP can do: analysis with RefSeq transcripts
By default, VEP uses the Ensembl/GENCODE transcript set when analysing your variants, but you can also choose to use NCBI’s RefSeq transcripts.
Continue readingCool stuff the Ensembl VEP can do: predict pathogenicity of missense variants
Some missense variants have significant impact on the protein function, some do not. In the absence of global comprehensive functional assays of missense variants, the next best way to assess if a missense variant is likely to be pathogenic is through prediction tools which take into account factors like the chemical properties of amino acids, functional protein domains and protein conservation to predict how likely it is that a missense variant will impact function. A number of different missense pathogenicity predictors are available for human through Ensembl VEP, and these are are optimised for different purposes.
New variant pathogenicity predictors
Rating variants for their potential deleteriousness is vital for solving the link between genotypes and phenotypes. There are many different algorithms for predicting how likely it is that a human variant would affect the function of a protein, and in release 94 of Ensembl, we’ll be making more of these available.