Download Diseased Gene sequence based on location ?

Question

[hafiz.talhamalik]

I am working on a disorder and I know mutations in the specific gene lead to that disease. Like GJB2 involved in deafness. I want to download all reported gene sequences (diseased) of GJB2 gene in the European population. How can I do that ??

[manaswwm]

I think maybe there is a more optimized way of doing this but one approach would be using ClinVar + the variation file from 1000G project (with some help from Ensembl). For example - you could start by shortlisting potentially pathogenic single position variants reported in ClinVar for your favourite genes. Using these single point positions in the genome you could try to find out its frequency in different populations - for example using this endpoint from Ensembl's REST-API. Caution - make sure that the reference genome versions on ClinVar and the endpoint from Ensembl are the same