The issue was found when importing patient https://preprod.phenomecentral.org/P0002926 to 1.3M5 instance.
Upon import, the patient JSON contains variants, however the gene field is missing and thus variants are not showing up in UI.
The original JSON as well as screenshots are attached.
Please notice the difference in JSON format between M1 and M5.
For genes we added id, so we have "gene" for for gene symbol and "id" for gene's EnsemblID.
For variants we removed "genesymbol" and added "gene" for storing gene's EnsemblID.