The logic is similar like the traditional gene knockout design. We want either delete the whole protein or mutate important protein domains. Unless there are important domains in the last exon, I do not recommend it. I prefer to choose the first 1 or 2 exons, which have a higher chance to cause frameshift or early stop. I will also try to run a westblot with antibody to verify the deletion efficiency. This will make life much easier.

If you want to knock-out a protein, I would rather target first exon, possibly close to the start codon. The "sooner" the frame shift happen, the better (I think..). I wouldn't reccomend using the last exon, since you might get a big part of protein to be functional anyway. The situation might be a bit more complicated if you are targetting a non-protein coding gene (like lncRNA).

Thank you so much @ Zengli Guo and Marta Kasprzyk .