Hi all.

I have detected somatic mutation and would like to know its significance for clinical interpretation.

I used MutationMapper in cBioPortal and then got a set of annotated mutations with plot as shown in below.

<img alt="lollipop plot example" src="http://www.cbioportal.org/images/lollipop_example.png" style="height:226px; width:297px" />

As you can see, there are a protein domains in the plot with yellow color and all the mutations are on its domain.

and my questions is below:

The segments that do not belong to yellow domains whose color is grey have no meaning for clinically annotating mutation? so I discard it unconsciously?
Your question is an important one without a definitive answer. In terms of clinical annotation, protein domain is just one of MANY, MANY potential features for prioritization. In practice, I would not discard mutations that are not in a known domain.