SwissVar: Clinically Relevant Protein Variations

In a previous post, I described ClinVar, the NCBI’s database of clinically relevant protein variations.  Recently, I came across SwissProt’s version of this database called SwissVar. SwissVar is designed to help you answer two questions:

  • What diseases is this protein involved in?
  • What proteins have been found to be mutated in a particular disease?

The following link will take you to the search page as shown below:

The SwissVar Search Page

The SwissVar Search Page

Enter a disease name or protein symbol to get started.  In my case, I started by looking for proteins involved in pancreatic cancer. At the top of the results page, you’ll see a Medical Search Heading (MeSH) term browser. This lets you refine the search in case the search term you used was either to broad or narrow.

Disease search result header

Disease search result header

If you scroll down past the header you’ll see a list of all known protein variants for pancreatic cancer.  To get more information on a particular protein, simply click on the protein accession.  The Entry name column, shows the UniProt symbol for the protein. The entry in the Variants column tells you the nature of variation.  In the first record, we can see that Alanine 476 was changed to a Valine.

A list of all known protein variants linked to pancreatic cancer.

A list of all known protein variants linked to pancreatic cancer.

Let’s take a closer at a variant record to see what kind of information is available.

Variant report

Variant report

Here we an see the position of the variant, the type of variant, how the variant changed the residue, and the disease that the variant was associated with.  To the left, we can see a navigation pod, that lets you quickly move to a particular section of the report.

Sequence information showing the location of the variation in the context of the protein.

Sequence information showing the location of the variation in the context of the protein.

 

 

In the Sequence information section you can see more information about the protein sequence, including the location of the change within the context of the protein.  You can see how well-conserved the residue is, making it easier to select a particular model animal.

Literature citations for the variation

Literature citations for the variation

Lastly we can see the literature citations that substantiate the claim associating this variation with a disease.

But what if we want to see all known variations (and disease associations) for a particular protein?  Starting at the main search page, we simply enter the symbol for the protein (in this case KRAS).

Gene-based search with relevant diseases

Gene-based search with relevant diseases

In the search results header, we see the same MeSH browser, but in this case, it shows us a list of all known disease types associated with mutations in KRAS.  If we scroll down further we see a list of all known variants.

Find all variants of KRAS.

Find all variants of KRAS.

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About aspenbio

I write software for scientists. I'm interested in Java/Groovy/Grails, the Semantic Web and Cancer Biology.
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