No, it's not a common expression. Usually, we would say something like 'You are my son, and that's it' or 'You are my son, end of story' in a more standard way.
It could mean that the person is simply stating a fact that the other is his son and that's all there is to it, like a final statement without further elaboration.
No, I haven't. I'm sorry. There are so many people in the world. It must be really worrying for you. Have you tried to contact the local authorities or put up missing posters?
Well, generally speaking, if it's a religious story related to the concept of Father (God the Father), Son (Jesus) and the Holy Ghost in Christian theology, it's about the Trinity. The Father is seen as the creator, the Son as the savior who came to earth in human form (Jesus), and the Holy Ghost as the spiritual presence that guides believers. But again, this is a very broad overview as there are so many nuances and interpretations within different Christian denominations.