Question about God's existence

My son is very uncertain of the existance of God and Jesus. We have always prayed together and have lived the word. Our family practices our faith. My son is 16 and isn't so sure now. I am alarmed but have really put myself in his shoes and tried to remember being 16 and had so many questions. I do remember the doubts and thinking it was all a bit of a fantasy I was supposed to buy into to. The only thing is I didn't really have a parent who nurtured my faith. What can I do? What scripture might I share with him? Please pray for him. He is young and I don't want him to turn away from the Lord. Am I over reacting? Is this just what pre-teens and teens go through? Please help!