NEW YORK (CBSNewYork) — A group leader of an after school program at a Bronx middle school is facing charges for allegedly sexually assaulting a 13-year-old student.

Detectives early Thursday morning escorted 24-year-old Michael Jenkins from the Bronx special victims’ unit into a waiting police car ahead of his arraignment.

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The students at the Angelo Patri Middle School know him as “Mr. Mike,” CBS2’s Janelle Burrell reported. He worked as an employee of an after school program run by a non-profit called East Side House Settlement.

According to police, Jenkins and the 13-year-old girl, who he knew from the school, had sex in his Bronx apartment on Monday.

On Wednesday, investigators say the girl told another employee at the school about the alleged encounter and that person called police.

Sources say investigators listened in on a controlled phone call between Jenkins and the girl, where they say he made incriminating statements, Burrell reported. Jenkins was arrested soon after.

“I kinda got teary because it’s too close to home,” said parent Gloria Pagan, whose 11-year-old daughter is a student at the school. She says she was considering having her daughter join the after school program, but now, she says “no way.”

“It’s not that the school is bad because they do have great workers there and everything,” she said. “Just maybe a mistake they did. They didn’t investigate too much on him.”

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Jenkins is not a city employee, but was cleared by both the city and state agencies hired to run background checks.

“The safety of young people is our top priority, and we take allegations of this nature very seriously,” a City Hall spokesperson said in a statement. “The individual was immediately suspended without pay and he is no longer permitted in any schools. DYCD has suspended funding for the program as we determine whether the provider can continue to operate at this school.”

“The safety and well-being of our students is our top priority and anything that undermines our mission of education and empowerment is completely unacceptable. We are supporting the ongoing investigation and will address the issue accordingly,” East Side House Settlement said in a statement.

Law enforcement sources say he does have prior arrests for marijuana, 1010 WINS’ Sonia Rincon reported.

Jenkins’ alleged actions have left parents and teachers at the middle school shaken.

“Hoping it’s not true, but if it is one of my students, I’ll be so devastated,” said teacher Donna Houman. “I love them like my own children.”

Jenkins faces several charges including rape, criminal sex act, forcible touching, sex abuse and acting in a manner injurious to a child.

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Police are investigating whether there are any more alleged victims, Rincon reported.