The state Senate’s latest budget proposal, which would wipe out $770 million in capital funding for the MTA, is putting mega-projects like the Second Avenue subway in jeopardy, agency Chairman Joseph Lhota said.

Lhota, in a letter to GOP Majority Leader Dean Skelos made public yesterday, said the proposal could even jeopardize a $3 billion federal loan the MTA is applying for, since it’s contingent on a fully funded capital program.