how to figure out if multiple benign mutations in one gene are harmful together?

I have found three coding mutations in one gene among my target population. I used three different softwares (polyphen2, sift, provean) to see how harmful these mutations are. all of them suggested that each of these mutations are not harmful (benign or neutral) on their own. but non of them showed any info about harmfulness of all of these mutations together.
Is there any way to get these softwares to tell me how bad all these mutations are together for this gene?
or would you please suggest any other software to figure that out?