As I understand God there is no separation of It to reality, and science doesn't disprove this but rather science is the study of God. As far as the God most people understand, monotheism over pantheism, many monotheists will say that the conditions science lays out before the Big Bang is also an explanation of God. It is still a mystery what really caused it, some people saying it was nothing, others saying it was quantum fluctuations, and others still believing it was God that caused the Big Bang. I've heard from monotheists the Big Bang proves the existence of God, whereas I've heard from atheists that it disproves this very same existence. The truth of the matter is probably somewhere between these extremes. Maybe it could be that God is not the quantum fluctuations but was the initial cause for these fluctuations to exist, taking a panentheistic approach to this mystery.