There are many factors that influence the potential outcome, size of the genes etc. Likely the missense in one will have little or no effect on the other (Nonsense mediated decay, if present, is posttranscriptional). The most likely influence on a nested pair is collision of RNA polymerases on opposites strands (see Hobson et al, 2012: http://www.sciencedirect.com/science/article/pii/S1097276512007708#). But collision presumes simultaneous transcription in the same cell type. This leaves many aspects that need some experimental data (transcription profiling in relevant tissue or cells) to determine the actual effect.

Dear Gerard,

Thanks a lot for your views and It really compelled me to think more deeper into it.