Multiple missense mutations in a single exon? - (Mar/14/2014 )

Just wanted to know if any one one had come across multiple missense mutations in a single exon for a single sample. 

Just got back my Sanger Sequencing results and one of the reads has like 3 missense mutations in a single read (both directions). These do not look like some artifact and have been very clearly called. So, just wanted to know what are the chances that something like  this might happen. 

Is this from cloning or what?

No, PCR product. Purified prior to sequencing.  But homozygous missense mutations observed in the middle of the read, in both directions

In that case, no, I haven't come across it. I have seen things like this with cloning, where the proper product is toxic, but somehow the bacteria have mutated the insert such that it no longer is toxic.

Is it possible that you are amplifying a pseudogene?