Scout: Right gene NOT saved for variants loaded with scout load region command

[northwestwitch]

Customer asked to load gene MICAL1 for this case: https://scout.scilifelab.se/cust003/19247

Command runned on hasta prod was this: scout load region --case-id keycaiman --hgnc-id 20619
Which results in this output:

So you imagine that 6 clinical SNVs should be found in this gene.

But filtering by gene in Scout you find none.

Searching instead by gene coordinates (chr 6, start 109765265, end 109787171)
You get these 6 (NO MICAL1)

The region looks busy by looking at the gene track on UCSC genome browser:

[northwestwitch]

Hi @4WGH, I've moved your ticket here. As a temporary fix try to search by chromosome coordinates!

[northwestwitch]

I'll look into this one today!

[northwestwitch]

Unfortunately I've been busy with other things and haven't had time to work on this issue

[jemten]

I'll look into it

[henrikstranneheim]

I took a look and I think that MICAL1 is not on the gene panels list and therefore not included in the select file that is loaded. However, it is present in the research file.

[northwestwitch]

I took a look and I think that MICAL1 is not on the gene panels list and therefore not included in the select file that is loaded. However, it is present in the research file.

Right! We need to upload from the research variants then! Thanks, Moving this back to Scout :)

[northwestwitch]

I misunderstood this. Closing this issue and reopening the ticket. The customer has the option to load research variants or rerun the case after adding the gene to a clinical panel.