2000 Other Saturn Models Could this possibly be something ot

Transmission problem
2000 Other Saturn Models 4 cyl Automatic 80000 miles

My son has a Saturn (I'm not sure of model or wheel drive type). Two days ago, it started hesitated when he went from 25 to 30 mph. Yesterday, however, it started making a clunking sound when it shifts into a different gear, or he puts it into reverse.

I called our local mechanic and he told me my son is looking at about $2,500 if they need to replace the tranny. He said though, that we should bring it in to be sure it is the transmission, as it could be something else.

Any ideas what else it could be with these symptoms?