What causes decrease in height?
The most common cause of this kind of height difference in a young person is wrong measurements.
If he hasn't had a fracture, it is unlikely that he lost the height from legs. Other way of losing height is by collapse of vertebrae.
Are you sure that the measurements taken was properly both the times ? If you are sure about it, we need to investigate further. I would advice to do an Xray of Pelvis including both hips as well as Xray of Thoracic and Lumbar spines A/P and Lateral views. This may possibly throw some light.
By the way, how was his puberty ( timing of facial hair growth and voice change etc). How is his facial and body hair growth etc now ?
It is unlikely to be due to heart problem. Usually height loss is due to collapse of vertebrae.
It is very unusual in a young person to have height loss due to vertebral fractures unless he is low in male hormones. That is the reason I asked about puberty and facial hair etc earlier.
It may be worth getting an Xray of pelvis as well as Lumbar and thoracic vertebrae as I mentioned earlier.
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