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openvar / variantValidator

Public repository for VariantValidator project
GNU Affero General Public License v3.0
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Stop codons not reported #535

Open leicray opened 11 months ago

leicray commented 11 months ago

Describe the bug Sequence variants that are predicted to create a new stop codon are not being reported correctly.

To Reproduce Validate any of the the following variants

Expected behavior In the case of the first variant, the expected predicted protein-level descriptions should be NP_065184.2:p.(Arg439Ter) and NP_065184.2:p.(R439*), but are being reported as NP_065184.2:p.(Arg439) and NP_065184.2:p.(R439).

Interestingly, variant NC_000001.10:g.26131710C>T maps to NM_020451.3:c.1315C>T and when that transcript-level variant is validated, the expected stop codons are not reported.

Counter examples The variant description NM_000088.4:c.2233A>T does validate correctly and display the expected stop codons. Similarly with the variant description NM_000088.4:c.2644C>T.

ifokkema commented 9 months ago

Cleaning up my email, I found this bug report. I can't reproduce it, though. Could it have been fixed already? It may have been related to the work on the selenoproteins.