No, optiplex 990 has cpu socket lga1155 and supports Intel 2nd gen cpu. I5-4690 is 4th gen cpu and requires different cpu socket lga1150. HD graphics 4000 is for Intel 3rd gen cpu ivy bridge such as i5-3550, i5-3570 or the like.  optiplex 990 chipset can technically support ivy bridge cpu if there is bios update,  It is not clear whether Dell has provided this critical bios update.  There appears to be some vendors claiming refurbished optiplex 990 with i5-3550.
I'm going to upgrade my cpu soon and I'm wondering if my 990 DT can use a Intel i5 4690 or if my 250 watt psu can use it? The cpu TDP is 85 watts.   If it doesn't, is there other i5s that have atleast an intel hd 4000 igpu that can work with the 990?
Can the Intel i5 4690 work on a Dell optiplex 990 DT