Create an offline Asset type Account, you could name it "Rental Security Deposit" or something along those lines, and put the deposit in there. It functions as a sort of "receivable" you expect to reclaim when you move out. Assuming you get it all back at move out you'd code it as a deposit in your checking Account with the offset being that asset Account you created. That would leave that Account a $0 balance and then you could Close/Hide the Account as you see fit.
If when you end the rental there is some sort of hold-back of some or all of the deposit, then in that Account you'd create the expense in the amount of the hold back. That would then leave the "net" receivable that you'd eventually record in the checking Account.
