We're having similar issues with 2yo DD at the moment (I've posted a couple of times before about concerns). Her weight has always tracked the middle percentiles, but her height has tailed off and she's gone from average to being on the 1st percentile for a good year or so, although it was actually only a year ago we realised how short she really was!
She has multiple food allergies, and although wheat seems to be the one affecting her the most, she has tested negative for coeliac disease.
We finally had an appointment at a growth clinic last week (referred to a larger hospital from a local paediatrician), and the consultant thinks she has a growth disorder 'look' about her, and so the next step will be another appointment in a few weeks to look at pituitary/growth hormone function, and then if a growth disorder is diagnosed, the next step may be growth hormone treatment.
It's taken so long to get this far - we had concerns about her height for a long time, but everyone said she would definitely catch up in a few months or that she was meant to be small. The growth spurt never happened, and myself and DP are average and tall heights respectively, so why would she be shorter than even a similar-aged child with short parents?
Trying to recall other things which are relevant - feet grow very slowly, and her feet are tiny and have perhaps grown one size this year. Her bones were x-rayed and her bone age was put at nearly a year behind her actual age. Her torso is big in comparison to her arms and legs and her tummy is very rounded, although before we removed wheat from her diet she was practically spherical (and endured a lot of unwelcome comments). Her weight is rather high for her height, but if she was the height we would have expected her to grow to, then she would be very much in proportion! Her diet is restricted but we are pleased to have got to a point where she's not having constant diarrhoea, as she did for a year after weaning.
Here's the weird thing though. I have a pituitary tumour myself, so both DD and I have regular endocrine appts, although no one has ever said the two are at all connected.
I've been mentioning to family members about the outcome being potential growth hormone treatment and was a bit dismayed when it was implied that we were 'interfering with nature' or making some sort of lifestyle choice, ie just trying to make her acceptably taller, but of course a growth disorder is so much more than your height - there are various other developmental issues as well.
OP - I'm glad you've got the referral now - the process of diagnosing anything is very slow, but good that you are in the system and can get DS properly checked out.