Most of the Mini-ITX boards available for either FM1 (AMD Llano) or Intel Socket 1155 (Sandy Bridge) will take 1 PCIe X16 card. This will be good for a single GPU system.
On the other hand the CASE that you plan to put that in is very important. For a high end GPU you'll need a CASE that will fit an ATX power supply and have a large space for the GPU card. I'd suggest This Lian Li or Similar: http://www.newegg.com/Product/Product.aspx?Item=N82E16811112265