follow-up on a significant variant/Gene

Question

[NB]

Hello,

With the help of sequencing and association studies, I now have a variant that shows significant association with the phenotype that is being investigated. But before, we jump into functional studies, I would like to know more about the functional impact of the variant and also the gene and its relevance.

Is there a tool, where I could visualize the protein structure and the amino acid substitution ? I tried SNPs3D and stSNP and Project Hope but none of the tools didn't work for my variant.

Also, I know that the Gene is involved in Insulin pathway, I would like to know if the gene is upstream or downstream of the pathway and what role it plays ? (not much of literature for this gene available in pubmed)

Many thanks!

[Devon Ryan]

You might give either SNPeff or Ensembl variant effect predictor a try. It won't show the actual structure, but it's a very convenient way to annotate variants to predict how deleterious they are.

[NB]

Thanks, Devon. Well, I already know that the variant is predicted to be conserved by PhyloP but with other tools such as Polyphen-2, SIFT its neutral. It may be helpful too visualize the structure..

[Devon Ryan]

It's mostly a question of whether the structure has been solved. Have a look at PDB.

Answer 1

[Robert Sicko]

I've not personally used it, but you could try MuPIT Interactive. For determining what role in the insulin pathway the gene plays you could try String