Address cases of multiple gene associations #8330
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@twhetzel
I think retinitis pigmentosa 7 should not have association with any genes. Please see my explanation in the comment. I can make the changes if you want, but I first want to make sure you have a chance you check my explanation in case you don't disagree.
src/ontology/mondo-edit.obo
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| @@ -271426,6 +271422,7 @@ is_a: MONDO:1040055 {source="https://clinicalgenome.org/working-groups/clinical- | |||
| intersection_of: MONDO:0019200 ! retinitis pigmentosa | |||
| intersection_of: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/10254 ! ROM1 | |||
| intersection_of: has_material_basis_in_germline_mutation_in http://identifiers.org/hgnc/9942 ! PRPH2 | |||
| relationship: excluded_from_qc_check http://purl.obolibrary.org/obo/mondo/sparql/qc/mondo/qc-multiple-gene-associations.sparql | |||
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I don't think this is correct.
According to OMIM, this record refers to the disease for which the RDS gene (PRPH2) is mutated, however, "A digenic form of retinitis pigmentosa resulting from a mutation in the RDS gene (179605.0004) and a null mutation of the ROM1 gene (see 180721.0001) has been reported."
Therefore, for this record, we cannot say that in 100% of the case, the disease is caused by a mutation in both genes (or in a mutation in only one gene).
The gene annotations should be removed for this disease.
Note: the definition for this disease should also be changed to make this disease concept not specific to the mutation in the PRPH2 gene.
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Thanks Sabrina. I agree and will make the changes.
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@twhetzel I updated the definition for retinitis pigmentosa 7.
I think this PR can be merged after QC have passed.
OMIM:608133 indicates that there are 2 included entries. We should add these with the "omim included" x-ref in a different PR (note, i have not created an issue for this).
From Trish - ticket added #8424
closes #8329
Please see ticket for explanation of changes