missense mutation [sf#295]

[srynobio]

Reported by pgaudet on 2012-01-18 16:34 UTC Hello, There are a few issues concerning missense mutations:

1. SO:0001583 : non-synonymous_codon should have as part of its definition 'non-sense mutation' (or stop gained), since that's a child.
2. It should be possible to annotate a missense mutation without specifying whether the mutation is conservative or non-conservative (since that concept is not defined in the ontology and there are different ways of defining this).

Thanks,

Pascale

[srynobio]

Response from @keilbeck

Hi Pascale These terms are worked out with the variant group at the EBI. After much discussion we have merged missense with non-synonymous. We don't have a history of adding the child terms to the definitions. I'm not sure what you want here. Do you have an example from the GO or something show me what you want. You can annotate to non_synonymous_codon without further specifying whether it is conservative or non-conservative. Stop gained and stop lost are kinds of non conservative, because by any scoring scheme, they are going to affect the protein. --K