Can you post a picture of your mobo?
This can not be possible had the motherboard been damaged from an over power draw. The system would have shut down... like pulling the plug... and refused to power on at all (no fans... nothing).
Because the PCIe slots are all powered by the same source... the motherboards power delivery. These are not separate sources for each PCIe slot. This same source powers everything in your PC... (Fans lights CPU RAM etc).
I own an 380X, and it throttles a lot, when I complain people tell me to raise Power Limit and link me to this post: AMD graphics performance
Funny now how this post might increase mobo deaths no?
Now people can see my original point: AMD should make their cards work out of the box correctly without people ever having to meddle with power settings.
You are wrong.
When PCPer asked a mobo maker about the RX 480 issue, the mobo maker replied the RX 480 likely will damage the PCI-E slot pins.
So the issue the OP described is perfectly possible.
My cynical self is telling me people are just taking advantage of the latest news and saying stuff like this to get free stuff
Remember when people were saying the new Crimson driver was frying their video cards?
Can you please provide a photo of your GPU and mobo and any additional proof you actually own the GPU and that slot is indeed not working?