I agree with PPs, it sounds like they will do a bone age scan. My dd has had a couple. After the 1st one, the endo said she is healthy, but petite and to focus on her self-esteem to make sure her size "doesn't get her down." That really isn't a problem because her size is a positive for her since she is a competitive gymnast. Now that she is about to turn 13 though I find clothes to be an issue. She wants to wear what her friends wear, but she is so tiny in the waist (I just bought her size 10 jeans) and for shoes she still wears a size 2/3, so it is slim pickens - at least she has her Uggs!
I opted out of doing the bloodwork because she didn't want it done. She is healthy, but very petite. I waited for the results of the bone age scan and decided if the results were wonky, then I might force her to have the bloodwork done, but everything was basically as I suspected.
When the results of the bone age are read you want the true bone age (the scan) to be less than what their actual age is. At the time that my dd had her last bone age, it read that of a 9.5 yr old when she actually was about to turn 12 two months later. This is good, it means that she has time to catch up to her actual age.
I know how you feel about the way it affect the kids in school and such, my dd has been there, but quiet honestly, if your child is for the most part healthy there isn't much to worry about. Genetic short stature is not the end of the world.
The endo will also go over the growth charts for you too. I don't know how they really work for a boy, but now that I understand how they work for girls, I understand more with my dd. With girls, most have their pre-pubescent growth spurt around the age of 10-11 and that is why all of dd's friends tower over her. When dd was 12, her body was that of a 9.5 yr old and she hadn't hit that growth spurt. Now I think this past yr I think she did have her pre-pubescent growth spurt, she grew 3 inches in a yr. In the past few yrs, she had grown .5" each yr.
As I said above, dd will be turning 13 in September - entering 8th. She is 4'6" tall and weighs 72#, but remember she is all muscle because she is in the gym 20 hrs a week.
Go see what the Endo has to say, but do the testing that you feel comfortable with. The bone age scan is non-evasive, but provides a ton of info for th Endo.