Probably under some remnant faction of the former Timurid Empire.
IOTL and ITTL the Timurids negotiated a peace with the Mamluks, after sacking and depopulating the Levant. Due to the autonomous nature of Mamluk households there's an uncomfortable rump Amir of Syria that looms just over the desert.
A Christian Egypt is huge. If the Venetians try to work with the Copts instead of converting them, they have a good chance of making Egypt the main possession of Venice, even above the Po Valley. Egypt requires naval supremacy to hold and Venice won't have to worry about naval supremacy for a long time. The organization of Venetian Egypt and the nature of their rule there will be one of the most fascinating aspects of this TL. I can see Egypt rising a lot sooner now that the pillaging Mamluks are out. Remember that OTL they weren't entirely removed from power until Napoleon invaded.
They do as all rulers of the Nile have to watch for invaders from the east, the hard part is trying to figure out the exact proportion of Arabs, recently-converted, crypto-Copts, Copts, Domari, Lebanese, along with the slither of all the other ethnicities. Official statistics are scarce/non-existent with Mamluk historiography being of little interest in the way of the focus on antiquity and Egyptian nationalism.
So Egypt is under Christian rule again for the first time in centuries. Interesting. I wonder if this will embolden any would-be crusaders to use it as a base to try their luck in the Levant again?
(Then again, they might be a little wary of doing that given what happened the last time the Venetians were involved in a crusade...)
There is a strong lobby for that and nothing stops individual captains from trying, Venice has more or less depleted the military-build up of the 1380s-1390s and is currently stretched thin, more on that later.