Thread by @ensembl

1/ Do you want to know if a variant will affect the structure and function of a protein?

We’ve got lots of tools and #data in @ensembl to help you investigate and we’re here to show you how! A thread...🧵

#genomics #bioinformatics # #tweetorial #Ensembltraining🧬

2/ If you are working with human 🧑‍🤝‍🧑 variation data, genome-wide variant deleteriousness rankings from the CADD algorithm are available as well as pathogenicity predictions from SIFT, Polyphen-2, REVEL, MutationAssessor and MetaLR for missense variants.

3/ You can see all this data in the ‘Variant Table’ page in the gene tab
👉 https://t.co/vZAsntjEXYensembl.org/Homo_sapiens/G…

4/ or the ‘Genes and Regulation’ page when exploring a single variant in the variant tab
👉
https://t.co/rvA0FRoVY1ensembl.org/Homo_sapiens/V…

5/ SIFT predictions are also available for cat, chicken, cow, dog, goat, horse, mouse, pig, rat, sheep, zebrafish and a number of plant species 🐈‍⬛🐔🐄🐎🐕🐐🐭🐷🐀🐑🐟🌱

6/ You can also visualise missense variants mapped onto the #protein structure in the Transcript tab. Just click on ‘PDB 3D protein model’ in the menu on the left hand side of the page to see if a @PDBeurope structure is available.

@PDBeurope 7/ If not, you can view the predicted protein structures from #AlphaFoldDB for human, mouse and zebrafish by clicking on ‘AlphaFold predicted model’ in the menu on the left hand side of the page.

8/ Missense variants are mapped onto the protein and can be colour coordinated according to whether the SIFT or PolyPhen-2 score predicts a tolerated or deleterious effect

9/ All of this is great if you are looking at previously identified variants already in the Ensembl database, but if you have your own set of variants, you can also retreive pathogenicity predictions using the Variant Effect Predictor (VEP) tool:


#VEP https://t.co/voGDKXirSJensembl.org/info/docs/tool…

10/ Read more about pathogenicity predictions available in Ensembl through the documentation pages: 👉 ensembl.org/info/genome/va…