Using Ensembl to explore genetic variations in the PKD1 locus

Open access genetic variation datasets in the EVA are fed into Ensembl where they are combined with many different data types from many different resources and services. These digestible chunks of information can be accessed via web browsers, or programmatically via the Ensembl API.

This means that we can use Ensembl to gain further insight into the genetic variations that are found within the human PKD1 locus.

For example, let’s look at the Ensembl table of variants view for PKD1 (Figure 4):

Figure 4 The Ensembl table of variants for PKD1 (view in Ensembl).

Viewing traits

There are a total of eight variants displayed for the human PKD1 gene (Figure 4). These have been filtered for pathogenic, exonic variants that exist at at allele frequency of greater than 0.001.

The pathogenicity of these variants within the human PKD1 locus can be further investigated with Ensembl by viewing the associated traits in the phenotypes section (Figure 5).

Figure 5 Using Ensembl to find traits associated with variants in PKD1 (view in Ensembl).

Here we can see that the majority of traits associated with variants in the human PKD1 gene are held privately at the human mutation gene database. The publicly available associations are mostly to polycystic kidney disease 1.

You can learn more about the variation data in Ensembl in our webinar Variation data in Ensembl and the Ensembl VEP.