Santana, whose real name is LaRon Louis James, was going through the screening at Terminal C about 6 p.m. when sources said agents discovered the firearm.
Sources said that once the "Love and Hip-Hop: New York" star was detected by authorities, he took off running and may have gotten in a taxi.
Port Authority Police Department detectives are currently looking for the Harlem-born performer, according to sources.
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The TSA didn't reveal the name of the rapper, citing privacy laws, but said that a passenger going through screening around that time had a gun in his bag. When the passenger realized the gun had been found, the TSA said the man left the airport, leaving his luggage and gun behind.