Shoe size is so much more complicated than just the length of the foot.
The ball to heel measurement, the instep, the shape of the foot, how high the arch is whether toes are squared or tapered etc... all of it and more has a bearing upon the size.
You will also find that different manufacturers will have their own sizings because the lasts they use to manufacture shoes will vary.
The way a shoe fastens also makes a difference - lace ups and slip ons will fit differently to velcro or bungee lace shoes.
It is more complicated than it first appears.
You need to get him properly measured by a trained shoefitter because his feet are not yet properly formed at 12 and no I do not mean by Clarks. The ridiculous machines they have never seem to get anyone's size right - the tiniest movement during the process will throw the whole measurement out.
Have a look at The Society of Shoe Fitters website ((www.shoefitters.org)) and find someone in your local area to go to. They will not charge for measuring and they will not insist you buy from them but they will have spent at least 1 year studying shoe fitting, the manufacture of shoes and the development of the foot (unlike most Clarks staff) and they are more likely to have more specialist equipment.
Your son probably needs measuring on a Brannock device as his feet are obviously on the larger end of the scale. Most Clarks shops don't have them but lots of independents do.
Sorry my post is a bit long - hope you get sorted out soon.