That same thing happen to me when I was 13 and when he turned 15 his voice will gonna be cool just like mine and they said those words to me that they can't understand me and now I'm super cool and invites me always to be the speaker in my campus cause they said I had an awesome deep male voice.. So mam don't worry..
If it keeps up and you are sure it is not just the natural consequence of puberty, you might see another doctor, one who specializes in puberty-related issues or possibly vocal-cord issues. Keep in mind that some people do have really unusual voices, and there is the chance that it's really just his voice. (Not a bad thing, deep voices in men are really impressive.)