The Education Department has opened an investigation into a Georgia school district, where a young girl alleged that she was sexually assaulted in a bathroom by a “gender fluid” student. (Gerry Broome/AP)

The Education Department is investigating whether a Georgia school system’s transgender bathroom policy, which permits students to use bathrooms that align with their gender identity, played any role in a young girl’s alleged sexual assault.

Alliance Defending Freedom, a conservative legal group, filed a civil rights complaint in June with the Education Department against City Schools of Decatur, and last month, the department wrote to say it was opening an investigation. The complaint outlines the girl’s allegations that she was sexually assaulted in a girl’s bathroom by a “gender fluid” classmate who was born male. The girl’s attorneys have accused school officials of creating “a hostile and discriminatory learning environment for girls” in violation of Title IX, which bars sex discrimination in public schools that receive federal funding.

City Schools of Decatur officials have contested the version of events laid out in the complaint, asking whether the assault reported by the girl did happened and contradicting claims that the classmate the girl identified is “gender fluid.” A social service agency investigation determined the girl’s allegations were “unfounded.”

The Education Department’s Office for Civil Rights investigates thousands of civil rights complaints every year. Depending on its findings, it can demand that school systems change policies or practices, threatening to pull federal funding if they do not comply.

The case in Decatur could have implications for school systems across the country as officials grapple with how to accommodate transgender students in school bathrooms and locker rooms. If the Education Department pushes the Georgia school district to abandon its transgender bathroom policy, other systems could do the same.

The battle over how to accommodate transgender students in public schools has been waged in courthouses, statehouses and in school board meetings, including in Decatur, where a group of parents assembled to oppose the policy and publicized the alleged sexual assault on their Facebook page.

Transgender students say that using the bathroom that matches their gender identity is critical for their health and well-being as they transition and that pushing them to use faculty restrooms can make them late for classes. But opponents of policies like the one in Decatur say they violate privacy and traditional values. In making their case, they have highlighted the specter of harassment or assault in restrooms, even though sexual assault experts have found no link between policies that accommodate transgender people and assaults.

“These transgender restroom policies are not working,” said Christiana Holcomb, an attorney with the Alliance Defending Freedom. “They are failing to serve and protect the privacy and safety of little boys and girls at school, and that’s not okay.”

According to the complaint, the girl, then a kindergartner at Oakhurst Elementary, reported to her mother in November that a classmate had pushed her up against a wall in a girls’ bathroom and touched her private parts. The classmate, according to the complaint, was known as “gender fluid.”

In the aftermath of the alleged assault, the girl’s attorneys say school officials treated the girl and her mother with indifference. They would not move the classmate the girl identified as her attacker to a different classroom. The Oakhurst Elementary principal told the mother that the school allowed students to choose what restrooms to use on the basis of their gender identity.

The complaint also alleges that school officials reported to the social service agency that they suspected the mother had sexually abused her daughter, setting off an investigation of the girl’s family.

The classmate “was allowed there because of the school’s new transgender restroom policy,” Holcomb said.

Decatur school officials have denied allegations laid out in the complaint, pointing out that police and a social service agency investigated the girl’s claims and determined them to be “unfounded.” School officials also contested the portrayal that the student the girl identified as her attacker is “gender fluid.” He is a boy and identifies as such, they told the news website Decaturish. Schools spokeswoman Courtney Burnett confirmed the details of the article to The Washington Post.

“We are aware of the unfounded allegations made by the Alliance Defending Freedom,” Burnett said in a statement. “We fully disagree with their characterization of the situation and are addressing it” with the Office for Civil Rights.

Under Title IX, school systems that receive reports of sexual assaults are required to conduct their own investigations to ensure that the educational rights of victims are safeguarded. Burnett did not respond when asked whether the district had conducted a Title IX investigation.

The Alliance Defending Freedom has campaigned vigorously against policies that allow transgender students to use bathrooms that align with their gender identity. But the argument that the policies endanger and violate the privacy of other students has not fared well in court.

Joshua Block, an attorney with the American Civil Liberties Union who has represented transgender students, said no federal court has ever agreed with the assertion that inclusive transgender policies endanger or violate the privacy of other children.

During the Obama administration, the Education Department sided with transgender students who argued that schools violated Title IX when students were barred from using bathrooms matching their gender identity. Now, students who are not transgender are increasingly arguing the opposite: that their right to privacy is violated by policies that affirm transgender youths.

In 2016, the Obama administration directed all public schools to allow transgender students to use bathrooms and locker rooms that aligned with their gender identity. Opponents immediately sued, delaying implementation of the directive.

Shortly after she was confirmed, Education Secretary Betsy DeVos, along with Attorney General Jeff Sessions, withdrew the directive. As a result, the department no longer investigates on behalf of transgender students who file complaints about bathroom access.

DeVos’s track record on transgender student rights has advocates concerned that officials will bring politics into their investigation of the case in Decatur, Ga.

“Our heart breaks for anyone dealing with the trauma of sexual violence, but there is simply no basis to the notion that policies protecting transgender students contribute to that violence,” said Gillian Branstetter, spokeswoman for the National Center for Transgender Equality, an advocacy group.

Education Department spokesman Nate Bailey denied that politics would play any role. Investigations are conducted by career employees, not political appointees.

“Politics play no role in OCR investigations. They are conducted within the strict confines of the law,” Bailey said. “It’s an unfounded claim and an unjustified attack on OCR’s dedicated investigators.”