Civil Partnership in Ireland?

Hi, my partner is born as a female but has changed his gender on his passport to male. However, in his birth cert, it is shown as 'female'. We fully understand that under the Irish Law, we cannot apply for a 'marriage' and therefore we went to apply for Civil Partnership. Unfortunately, we got a call from the registrar and she told us our application cannot be proceed and that is because my partner's gender is not the same in his birth cert (female) and passport (male). She rejected our application even though it is a civil partnership we were applying for. I need some serious legal advice on this issue. Is there any legislation stating that we are not allowed to be registered if the gender on the passport and birth cert is not the same? Plus, the registrar mentioned that if we ARE allowed to register (civil partnership), she is not uncomfortable doing the registration for us! Me and my partner were very offended by that.