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According to this verse: 049.013 Humans are created out of female and male. Yet there are humans who have functionally both sexes/genitalia. They are called hermaphrodites. Where do they stand in the Quran? Or perhaps they are not recognized in the Quran?

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Definitely the Holy Qur'an is aware concerning everything. As a general rule, the Holy Qur’an mentions many issues in general. Accordingly, we cannot accuse it due to the exceptions. On the other hand, in regards to your question that asked:

Where do they stand in the Qur'an?

As far as I know, in such cases as you mentioned, usually one gender is considered as a prevailing (although he or she has the other gender sign as well). Then, the response can be the prevailing one. (Based on my opinion).

On the other hand, you and many other dear individuals ought to pay heed to this significant issue that the Holy Qur’an has named many significant matters, but it has not mentioned many other matters as well. Actually it is approximately 604 page, not e.g. 100.000 pages to explain everything, and rationally in that case just few limited people would refer it due to its length. In fact the Qur'an can be considered as a general book which indicates many specific matters as well, but it doesn’t mean that it must explain everything, otherwise we can name many many items which are not (directly) indicated in it. Then, we should look at the issue fairly. I hope my explanation is persuasive. Good luck dear mate.

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    Nice answer, hope this reaches others as well! because there are a lot of Muslims out there who believe that just because something is not explicitly mentioned in the Quran that may make it permissible or impermissible! – Aboudi Feb 25 '16 at 13:33

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