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exomiser / Exomiser

A Tool to Annotate and Prioritize Exome Variants
https://exomiser.readthedocs.io
GNU Affero General Public License v3.0
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No known disease #576

Open pnrobinson opened 1 week ago

pnrobinson commented 1 week ago

If Exomiser ranks a variant in a gene not associated with a Mendelian diseases, it shows this

No known disease

The next two messages do not make sense though

Gene scores under compatible inheritance modes:

If there is no disease, then there is nothing for an inheritance mode to be compatbile with

No phenotype matches to diseases with this MOI.

Again, there is no disease here.

These message could probably just be deleted from the output, everything else would still make sense.

damiansm commented 1 week ago

There may be mouse, fish or PPI phenotype matches under the different inheritance modes though, each with a different score. Maybe "compatible" is the wrong word here though. We are trying to convey compatible with the variant, i.e. if it is a chr1 het variant it is compatible with an AD mode of inheritance.

On Wed, Oct 16, 2024 at 2:01 PM Peter Robinson @.***> wrote:

If Exomiser ranks a variant in a gene not associated with a Mendelian diseases, it shows this

No known disease

The next two messages do not make sense though

Gene scores under compatible inheritance modes:

If there is no disease, then there is nothing for an inheritance mode to be compatbile with

No phenotype matches to diseases with this MOI.

Again, there is no disease here.

These message could probably just be deleted from the output, everything else would still make sense.

— Reply to this email directly, view it on GitHub https://github.com/exomiser/Exomiser/issues/576, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABHO4PAJIR44WFYPUPNDR3TZ3ZPR5AVCNFSM6AAAAABQBNLKX2VHI2DSMVQWIX3LMV43ASLTON2WKOZSGU4TCOBSGI2TMMI . You are receiving this because you are subscribed to this thread.Message ID: @.***>

pnrobinson commented 1 week ago

I see - yeah, that makes some sense, but for a new diseases whose MoI is unknown, we do not really know if two variants are both PATH (and it is AR) or one is PATH and one is BENIGN (and it is AD). It seems more intuitive just to show the variants and mark the gene as hypothetical or candidate or something??