It isn't your motherboard because if other PCI-E x16 slots aren't working, that isn't a coincidence. If you are still able to get the computer to post, obviously the motherboard is capable of powering on and adequately powers and controls the CPU and RAM. If your PSU was the sole cause, you'd most likely experience your computer having a burning smell, or you wouldn't be able to turn it on, or in most cases, your power supply will surge protect itself by turning itself off then on when trying to power it on.
If your computer without the GPU is able to post for an extended period of time without immediately powering off, it's fine.
If you want to be positive it isn't your motherboard, you can always try:
https://forum-en.msi.com/index.php?topic=31222.msg178956#msg178956
A good bet is this:
The GPU was probably receiving inadequate air flow (can you smell a bit of burning?) and therefore overheated, the GPU failed while being powered on, causing drivers to crash and your OS to malfunction, this probably gave you a BSOD and could have messed with many other factors (windows immediately shutting down is bad for you kids).
RMA your GPU for free, your vendor will test it for you and let you know if there are any issues, if there are, chances are you will get it repaired or replaced for free.
If the issue stays, swap out parts until an issue is found. No point playing a guessing game.
@Professor Pericles