Apparently, Nathanael knew of the prophecy at Micah 5: 2 and considered Nazareth too insignificant to be the Messiah’s hometown.
كَمَا أَنَّ وُجَهَاءَ ٱلْيَهُودِيَّةِ ٱحْتَقَرُوا يَسُوعَ لِأَنَّهُ مِنَ ٱلْجَلِيلِ .‏