A boy who spent all his life believing he was weak, suddenly discovers that there is something, something special about himself. He never understood until he fell 1200 feet off a mountain during a trek; and survived without a scratch.

You've repeated the word "Something", so correct that. About the logline itself, you've better go back and improve on it. It reads as an event, and it doesn't really reveal the goal and the conflict he must face/overcome. May this also help you in your process.

"A boy who spent all his life believing he was weak, suddenly discovers that there is something, something special about himself"

This could potentially be a tag line for marketing purposes but shouldn't be in the logline.

It seams that falling off a mountain is a significant enough an event to suffice for an inciting incident. In my opinion start the logline with:
After a boy falls 1200 feet off a mountain and survives without a scratch?

Only you will need to come up with a goal that correlates to this inciting incident appropriately.

Hope this helps.

What does he do with his super powers? What stops him? What must he overcome to reach his ultimate goal?

That is the story. You have an interesting marketing line.