All the old PMA250 versions had a phono stage so unless a previous owner has removed it (whcih would be bizarre) then yes it has one. In fact as you are getting sound out of your TT it must do. I take it you have tried increasing the volume on the amp? Phono will sound a lot queter than the line level inputs for the same pos on the volume scale.
Otherwise check out your catridge - is it fitted correctly, all connections tight etc?
If nothing wrong there could be a fault on the amp
Current Lash Up:
TEAC VRDS 701T > Sony TAE1000ESD > Krell KSA50S > JM Labs Focal Electra 926.