You can also try Fancy Gene.

I strongly suggest you learn a little bit of SVG to do this. SVG images are easily edited with Adobe Illustrator, and can be visualized in many web browsers.

Basically, you need to set up a coordinate system for your genes/exons and mutations. Learn how to draw some boxes and lines with SVG and you will quickly see how easy it can be.

if your protein is available as a genbank file, save it as XML and process it with XSLT and the following stylesheet: https://github.com/lindenb/xslt-sandbox/blob/master/stylesheets/bio/ncbi/gb2svg.xsl

xsltproc gb2svg.xsl protein.xml > protein.svg

it should prepare a SVG file that you can later modify with inkscape

You can see an example of how this is done in Alexa-seq using R code. The figure shows LAMA3 with 77 exons. There are two representations of the gene, one that shows the overall structure of exons and their proportional distance and the other has a sort of zoomed in view with exons depicted on log2 scale and introns on log10 scale. In this case some alternative splicing information is marked up. But instead you could indicate mutations. Unfortunately this is not part of an existing R package and is just done with basic R plotting functions in an R script of about 300 lines. But, maybe it will give you some ideas.

If it is an eukaryotic protein and if there is a genome available (at diArk), you can try WebScipio.