One of the District’s highest-performing charter schools is under federal investigation amid allegations it more harshly disciplines African American students.

The Education Department’s Office for Civil Rights launched a probe into potentially biased discipline practices at BASIS DC — a middle and high school in downtown Washington with a long waiting list. The school, known for its rigorous academics, is part of an Arizona-based chain of charter schools.

Education Department spokeswoman Elizabeth Hill confirmed the probe but said her agency does not comment on open investigations. The investigation aims to determine whether the school’s disciplinary practices violate the Civil Rights Act of 1964, which prohibits discrimination on the basis of race in any program or organization that receives federal funding.

Phil Handler, a spokesman for BASIS, said the charter network does not comment on ongoing investigations. But he said the school is cooperating with the civil rights office and is “committed to providing a learning environment free from discrimination on any basis.”

In June, The Washington Post reported on a school lockdown at BASIS DC. Yumica Thompson — the mother of a middle-school-aged African American boy with special-education needs who attends the school — told The Post that an adult summoned law enforcement after her son and his friend, who is also black, yelled “shoot” across the hallway.

The boys said they were excited about plans to play basketball at a nearby recreation center after school, while a staff member thought he heard the students exclaiming they were “gonna shoot up the school.”

The students were questioned by police without their parents present, and a sergeant with the federal Joint Terrorism Task Force was on the scene.

The incident was written up in each student’s file, though they received no further disciplinary action.

One student’s write-up, which was shared with The Post, said staff members advised him to “be mindful of using broken English or slang” because his words could be misconstrued.

Thompson lodged a complaint with the Education Department about the incident and said her son had been removed from class for discipline issues more than 80 times during the 2017-2018 school year.

With help from Advocates for Justice and Education — a legal advocacy organization — Thompson and an attorney expanded the scope of her complaint to allege that many black students are disciplined more frequently and harshly than their white peers at the school. The Education Department also has an open investigation into an allegation of employment discrimination at ­BASIS DC.

“Race-based discrimination in the District’s public education system still persists, and every day students of color are systematically pushed out of schools, particularly some of the District’s ‘highest performing’ schools,” said Stacey Eunnae, an attorney at Advocates for Justice and Education who worked on the complaint.

Eunnae said in an interview that BASIS DC has created a culture that discourages students of color from enrolling or remaining in the school. Between 2012 and 2018, the BASIS DC student body has grown from 443 to 602 students, according to city data.

But during that same period, the percentage of students who are black shrank from 55 percent to 37 percent. The white student population grew from 28 to 39 percent, and the Asian population increased from 4 to 8 percent. The Hispanic population remained similar at around 7 percent. Children who identify with multiple races account for the remainder of the student body.

Citywide, the percentage of students who are white has grown, while the percentage of students who are black has declined, though the change has not been as drastic as it is at BASIS DC.

At BASIS DC, 13 percent of black students and 2 percent of white students received out-of-school suspensions, according to city data. Ten percent of Hispanic students received out-of-school suspensions.

Five percent of black students and 4 percent of Hispanic students received in-school suspensions, compared with 2 percent of white students.

Black and white students have similar re-enrollment rates, city data shows. Eighty percent of black students and 83 percent of white students re-enrolled last year

The D.C. Council voted to overhaul the city’s discipline policy last year, restricting the circumstances when a school can suspend or expel a student.

The move was an attempt to address dramatic disparities in discipline rates among black and white students.