Mutations for entire genes missing

In comparing the OmicsSomaticMutations mutation data between 23Q4 and 23Q2 I’ve found that mutations for multiple genes are now entirely missing. For example all mutations in RAB10 (9 non-silent mutations) or DAXX (50+ non-silent, including the homozygous p.G416V in ACH-000929) are totally missing from the 23Q4 files.

What is the reason for these mutations being removed?

Also, RUNX1 mutations do not appear in the portal view, but do appear to be in the files.

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We updated our mutation pipeline in 23Q4 to improve our annotation and germline filters. It is likely that some mutations are lost because they are now identified as likely germline variants. Please refer to our documentation for details on our updated pipeline.

To your second point, it turns out this gene was mapped to an Entrez ID (100506403) in the genomics pipeline that’s different from the portal’s id mapping (861). We are currently working on unifying the id mapping across various processing pipelines in DepMap in the hope to eliminate this kind of mismatches, but it is going to require some time.

Thanks for bringing this to our attention!