New York City’s public school district is set to lose millions in federal funding after missing the Trump administration’s deadline to change its policies on transgender students in compliance with Title IX.

The Department of Education gave New York City Public Schools until the end of last week, Politico reported. The deadline was then extended to Tuesday at 5 p.m. after the city asked for a 30-day extension, which was not granted. Now past the deadline, the city is set to lose roughly $50 million.

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The funding in question is $15 million for the city’s five magnet school programs for the next fiscal year, starting Oct. 1. An additional $36 million for the remainder of the grant period is also being pulled.

The Department of Education previously said the move does not apply to existing money.

The federal Magnet Schools Assistance Program provides grants to state or city education agencies for creating or improving magnet schools, which cater to students of diverse racial and socioeconomic backgrounds. Unlike traditional public schools, magnet schools are free for families.

Previously, acting Assistant Secretary for Civil Rights Craig Trainor put New York City Public Schools on notice for policies amounting to sex-based discrimination.

The policies under scrutiny allowed transgender students to use facilities, such as restrooms or locker rooms, that align with their gender identity instead of their biological sex.

They also allow students to play for sports teams or participate in activities in accordance with their gender identity, which Trainor said includes overnight field trips where students of the opposite sex may sleep next to each other.

Last week, a lawyer representing the New York City Department of Education asked Trainor in a letter to extend the Title IX deadline by a month so that the federal department can “explain the nexus between your interpretation of Title IX and the [magnet school] grant funding that is being discontinued.” The letter says the move “has deprived the NYCDOE of the procedures and due process required by federal regulations before discontinuing funding based on alleged noncompliance.”

New York City Mayor Eric Adams has denied that the Trump administration’s funding threat motivated his recent decision to review the city’s policy that allows students to use the bathroom of their choice based on gender identity.

“I don’t know what parent of a little girl would be comfortable with a boy walking into the shower where their baby is,” he said on Monday. “I’m just not going to support that.”

In addition to the school district in New York City, Fairfax County Public Schools in Virginia and Chicago Public Schools in Illinois are expected to lose $3.4 million and $5.8 million in federal funding, respectively, according to the New York Post.

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The other two school districts have similar gender policies in place and were subject to the initial Friday deadline that New York City’s education system faced. Each reported school district that received Trainor’s warning was given 72 hours’ notice.

The Washington Examiner contacted the Department of Education and New York City Public Schools for comment.