Since you and your son are Joint Tenants, it would be assumed that each of you contributed 50% to the purchase.
As you paid the down payment in full, yes, the 50% that he would have paid would be a 'gift' to him from you.
Since a Gift Tax Return is filed separately and is not reported on your personal Form 1040, you can download Form 709 from the IRS site and send it in. It doesn't affect your taxable income at all.
When you sell, since both names are on the Deed, you will each report 50% of any Gain (no loss is claimed on sale of a personal residence). However, with the Home Sale Exclusion usually the sale is not even reported on a tax return.
Here's more info on the Gift Tax.
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