Download or subset pathogenic variants for a selected gene from ensembl

Question

[victor.lorca.castellanos]

Hello,

I need to plot Lolliplots, trackviewer for a selected gene.

I am a principiant Rstudio user. I want to create a lolliplot that shows pathogenic and probably pathogenic variants in APC gene, which are described in ensembl database. I want to export this file in BED format, but I can not download only these types of mutations (I can download all mutations, including benign variants, but I can not filter it).

Can someone help me to download and load these files in Rstudio?

Thank you so much,

Víctor.

[Emily]

When you say "pathogenic" do you mean actually pathogenic in the clinical sense? That is, annotated by ClinVar based on the observation of the variant in connection with a clinical phenotype? Or do you mean predicted to be pathogenic based on loss-of-function of the gene?

[victor.lorca.castellanos]

Hi again, I am referring to pathogenic variants in the clinical sense. Thank you so much!

[Emily]

Two options, use the table as genomax suggests and filter to show only pathogenic variants. Click Filter other columns -> Clinical significance -> choose all that are relevant to you then download the table.

Alternatively, you can use BioMart. Use the short variation database, filter by the gene ID and clinical significance, then get whatever you like as attributes. This may be the easiest way to get what you need in BED format as you can choose which columns you get in your output yourself.

Answer 1

[GenoMax]

You can find exonic variants for APC gene on this page (scroll down to see variant table). You should be able to filter the table using available filters. You can then download resulting table by clicking on icon at top right of table to get a csv format file.

If you need to download all variants then use BioMart at Ensembl.

Answer 2

[Emre]

https://digibio.blogspot.com/2017/11/clinical-signifiance-and-variant-effect.html