Ah Yes - One of the great questions of the Age.
Why does God “Allow” this or that negative thing to happen.
We don’t understand but somehow we think we should understand.
Jesus answer as quoted by Todd is probably the best you can receive.
It is a good answer because it, like many of Jesus teachings, forces us to examine ourselves. For instance, my wife who holds a RN, MS, and MBA developed Alzheimers Disease 6 years ago. Why would God do this to her? Why would he reduce her to the level of a two year old? What good is this (or any other terminal disease) in God’s Love?
Well let me briefly share what "Good has come of it. It stirred us both to return to the Church. It has taught us both complacency in God’s will. I have learned more about patience, endurance, Love, sincereity, friendship, faith, perseverence, and the power of prayer in the last about 4 years than I learned over my entire life up to that time.
We cannot tell you for sure whether God “causes” birth defect, or if He “allows” them or why. What we can tell you is that those born “misformed” provide a great and powerful opportunity for the rest of us to demonstrate and learn of how God’s love flows through us into the world.
Peace
James