Why would an (otherwise healthy) young boy have a permanently gravelly voice for his whole life?
Both this article from a prominent children's hospital mention a wide variety of causes. Another less formal article, but also from a highly reputable children's hospital mentions some causes, but none that could explain a life-long condition.
Since we're talking about a life long condition, and no known trauma to the larynx, it seems reasonable to assume that a physiological abnormality is at play.
What physiological causes would be among the most common?