Welcome to HCM.
At the age of 13, sometime adolescence yet to be started in some individuals. So you might not be able to appreciate the development of penis. Moreover if your son is a little bit obese
and his pubic pad of fat is more (familial), then also the penis seems smaller and sunken.
You can also go for an estimation of testosterone
in his blood (hormone). It must be between
8-53 ng/dl. If it is lower than that you have to start treatment as early as possible. If it is abnormal then you can also opt for Karyo-typing. That also will give information about the genetic constitution of your son.
Get cleared as soon as possible.