The 17-year-old pupil, who could not be named as she was a minor, was expelled from Madrasah Mueinul Islam earlier this
year, ostensibly for breaking the school's code of conduct.
But the girl's family filed a complaint to the commission last week, saying the school took issue with her after suspecting that she
may be homosexual.
The pupil's family said: "We  request the entire school must be investigated and all the children must speak up as they are being
victimised .
"This is not Islam and as a higher learning centre for pupils to learn Islam they should be the example of how Islam should be followed and all the girls who have been expelled before by being falsely accused of being lesbian should also be cleared."
The school's principal, Mahmood Ismail denied the teen's expulsion because of her sexuality. Not wanting to divulge any details, Ismail said the pupil was expelled for contravening the school's code of conduct, though he could not refer to which part of the school rules she had broken.
"Obviously the allegations of lesbianism were totally denied.
Even the word lesbian was never even used at any point in the disciplinary process. It was rather the complainant who had used the L word multiple times in conversations," said Ismail.
"At the time he was reprimanded by the head of the institution and told not to use that word."
The pupil was expelled before she could write her final exams this year, and she was only allowed to write them after her parents intervened.
According to her, teachers began accusing her of having sexual relations with another pupil at
the school last year. She was forbidden from socialising with the other girl after teachers humiliated them in front of other pupils by
announcing their alleged affair.
"I don't know how to feel because even if I do go back, I don't know how they will look at me and they are accusing me of being
something I am not," said the pupil.
According to SAHRC provincial head for Gauteng, Buang Jones, the commission received the complaint from the family last week, and the institution's legal team had begun the investigation.
"Private schools are also subject to the same constitutional scrutiny and have to abide by what the constitution says regardless of religion," he said.
A letter from the commission to the school was shared with The Citizen this week. In it, the school is invited to respond to the allegations it discriminated against the pupil.
"After careful assessment, the commission has found that the complaint falls within our jurisdiction as there is aprima facie violation of the complainant's right to dignity (s10) and freedom and security of the person (s12)," the letter read.
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