Check out MetaDome

[moonso]

MetaDome is a tool that scores positions based on how sensitive the position is to changes. Similar to pLi but it uses the information from protein domains combined with variant frequencies. We should investigate if we can score variants and include in rank model or at least link out to the web based tool.

MetaDome is a fast and easy-to-use web server that offers an easily accessible and unique perspective that enables researchers and clinicians to interpret variants of unknown significance via 'meta-domains'; a concept that we have previously validated ( L. Wiel et al. Human Mutation, 2017 ) which makes use of protein domain homology within the human genome to transfer genetic variant information across homologous domains. MetaDome can visualize meta-domain information and gene-wide profiles of genetic tolerance.

Browser: https://stuart.radboudumc.nl/metadome/
GitHub: https://github.com/cmbi/metadome

[dnil]

Downloadable data is now available! See laurensvdwiel/metadome#54 (comment) and https://zenodo.org/record/6625251.

[fulyataylan]

I think having a link and the gene name inserted is enough. Then the user can pick the transcript. I think you don't need to spend so much time on the transcript part. I have been using this tool lately and I found it useful to see the constraint parts of the proteins.

Many thanks @dnil for taking the time to explore this again!

[dnil]

And how would you go about doing that?

[dnil]

We could help them with a PR for like laurensvdwiel/metadome#63 I suppose, but then they have to deploy it etc, and they haven't really updated in a long time...

[dnil]

Actually there has been a bit of activity; LvdW is at Stanford now it seems, but has made contributions to https://github.com/laurensvdwiel/MetaDome-vcf-annotation rather recently. Which would fit a pipeline well, and we could pick up the annotations from there.

[fulyataylan]

That is great!