On standard motherboards (normal CPU socket placement) usually it will clear the first PCIe slot as long as the coolers width is 140mm or below, this has been my experience on my TJ08-E (micro ATX case) with multiple micro atx motherboards, that usually have the 16x PCIe slot on the first pcie slot. The ninja has 135mm from what i can tell on the specs, so if the GA-Z170X Gaming G1 has a standard socket and the measurements provided by scythe are also accurate and it doesn't have a huge backpalate or screws coming in the back, then i think it should be fine.
Thanks I was originally looking at the Noctua but I noticed the Scythe gave me 5mm more of clearance.
If you wish to go with noctua, look into the S models, the newer revisions were done to have enough clearance for the first PCIe slot, thats if the motherboard has the standard socket placement, kinda like thermalright Silver Arrow that its also asymetrical which makes the widest part be oposite to the gpu and leave the 70mm side (from center to side) to the side of the GPU.
Do you mind me asking why going for that motherboard is extremely expensive, given that has some nice addons like the Creative Sound card, you will still have less spent going with the seperate sound card. If you are spending that high on the motherboard consider the X99.