Nefertiti's eye is little bit unique with different syndromes.
Nefertiti's eyes are quite unique. It becomes clear that we are looking at something different, something more real. The inner canthus (the corner of the eye near the nose) descends abruptly and abuts the upper eyelid, Both Nefertiti's finished eye and empty socket show this form. the artist of her famous bust Thutmose, clearly intended to include this in his work.
The art style of Nefertiti's period was known as "Amarna Art" which focuses more on realistic features and naturalistic depiction. So it is likely that the eye shape as opposed to a stylised rendering. It could be that Nefertiti had an epicanthic fold, a piece of skin from the upper eyelid which converts the inner edge of the eye.
This type of eye trait can be found in people suffering from different syndromes, some of which are genetically based. So, her unique eyes could be a real reflection on a physical condition. There is also some suggestion that Nefertiti's unique eyes were later used as sort of "Royal Market". Thutmose may have created later works of art using this artistic convention in other depictions reserved only for royalty.