While a linear transcript view can provide some context for how a mutation will affect a protein, it doesn't substitute for viewing the mutation in the actual 3D protein space. We use the MuPIT 3D protein viewer from Rachel Karchin's lab at John Hopkins to provide this visualization to our users.
Access this tool by going to our Visualization tab and following the wizard to enter your mutation data of interest into the Visual spreadsheet, which is our default view. Please make sure to choose 'Somatic mutation (SNP and small INDEL)', not 'Somatic non-silent mutation (gene-level)'.
Once you have the mutation data you're interested in, click the caret menu at the top of the column and chose 'MuPIT View'. This will send your mutation data to MuPIT and open their viewer in a new tab.