...Our first clue to the fact that Nathanael was a scholar of the messianic prophecies is his comment regarding Nazareth. He knew that scripture clearly taught that the Messiah would be born in Bethlehem, but wasn't so sure about the Nazareth connection.
[The prophecy regarding Nazareth is a bit more hidden (Isaiah 11:1 speaks of the branch, which is netzer in Hebrew, and the town of Nazareth, (netzret in Hebrew), means "branch town").]
When Yeshua first spoke to Nathanael, He was referencing the second part of Isaiah 53:9:
Because He had done no violence,
Nor was any deceit in His mouth.
Yeshua was not calling Nathanael righteous. Yeshua was quoting the very prophecy that Nathanael had been studying, in order to emphasize that He Himself was the Messiah."