TMZ broke the story ... ballistic testing on the .40 caliber Glock found in Compton -- back in 1998 -- showed it matched the one fired in the 1996 Tupac shooting. The mystery was where the the gun went after that testing. Neither LA cops nor Las Vegas cops knew for sure, but we've learned the feds actually had it last ... and it's been destroyed. Now here's why.

ATF agents did the testing in 2006. While it did come up as a possible match for the Tupac weapon, it also possibly matched another unsolved case in Las Vegas ... according to ATF spokesperson Ginger Colbrun. She tells us the ATF then sent the weapon to Vegas.

Multiple law enforcement sources tell us LV Metro PD conducted its own ballistic testing, and here's the big let down -- they determined it was not a match for Pac's case. It did match the other unrelated case, but police had no need for the handgun, so in 2006 they sent it back to the ATF.

The Glock sat in storage until 2013 when the ATF was taking inventory.

Colbrun says as part of standard ops, the agency decides what to do with items after a while. They checked with Las Vegas cops, who signed off on the weapon being destroyed ... and it was, along with a stockpile of other unneeded guns.

It's gone. That's it. Case NOT closed.