ANSWER: The question of what the Bible says about birth defects and why does God allow them to exist is a tough one to handle, especially for parents who have children with disabilities. We have autistic problems in our family and therefore can relate to your situation with your Asperger's syndrome son. Birth defects, though generated because of sin, are NOT the full answer. God has chosen to allow sin and its consequences for a very special purpose. The plan of God, only begun in Genesis, is for man to fully be "in his own image" (Genesis 1:26).
God gave our first parents free choice to eat of the Tree of Life or the Tree of Knowledge of Good and Evil. They chose to eat from the wrong tree. The Bible records they wanted to define and decide for THEMSELVES what was right and wrong - instead of trusting God. By rejecting God, they put themselves under the influence of his adversary, the devil.
God, since the time of Eden, has chosen not to interfere in human affairs unless it is to fulfill a particular purpose. Your son needs to understand why God does not get involved in human choices. By God keeping His distance, he is allowing us to experience the full effects of our choices and to learn many valuable lessons.
Just like God, our choices can affect others. Poor choices by one person can cause the suffering of others! For example, if a mother takes illegal drugs during her pregnancy there is a much higher risk her innocent baby will be born with disabilities. God allows this to happen to bring us to Him and to understand sin always affects everyone.
Sometimes people are born with physical or mental defects not because of the wrong choices of their parents or ancestors, but because it fulfills the will of God. Jesus' healing of a man who was blind from birth is a striking example of how God accomplishes his goals.
Christ was walking with his disciples one day when he saw someone who was sightless all their life. The disciples, who assumed that certain diseases and afflictions came on a person as God's punishment of sin, asked whose sins the man was suffering for. Jesus' swift answer challenged their assumptions regarding suffering and how God accomplishes his will on earth.
Jesus answered, 'His blindness has nothing to do with his sins or his parents’ sins. He is blind so that God’s power might be seen at work in him. ' (John 9:3).
Here was a man who, through no fault of his own, his parents, his grandparents, etc. was born without sight. He no doubt struggled doing everything he needed done as a human to live. At that time (and for many years after) being born with such a disability virtually guaranteed a person a life of suffering, poverty and rejection. Yet, all that happened to him led to this moment where the mighty power of God, through his Son, would be displayed as a witness to the people and recorded in the Bible for others.
In Ephesians 3:15 the apostle Paul states that God is building a family. His purpose is to have humanity become His spiritual sons and daughters. God is reproducing Himself by building a family where Jesus is the firstborn (Romans 8:29, Colossians 1:18). Explain to your son that his disabilities (defects) have NOTHING to do with what he has done. In reality, we all have disabilities of one kind or another with varying severity. All these human problems God allows so that we will ultimately choose his way and reject the way of Satan.
I have found that many times those with the greatest disabilities, especially those with birth defects, draw closer to God and His ways than others who seem to have fewer problems. We also need to keep praying to ask for the help we need to deal with our disabilities and keeping reading the Bible to better understand His will. He will answer us in such a way that will bring glory to him.