Its difficult for me to interpret the extensive testing your son has had with the above information.
I will make a few comments though - I wonder was electron microscopy of the skin or muscle biopsy done? sometimes some metabolic or mitochondrial disorder may be more apparent on electron microsopy of the tissue sample (a very high powered microscope able to look even at individual cells)
Other enzymes can be tested in the muscle biopsy sepcimen which disorder of can give exercise related cramps, discolored urine etc - myophoshorylase or adenylyl cyclase are some examples. Other muscle disorders can be diagnosed from the muscle biopsy such as muscular dystrophy
If the urine changes color to red during excercise or the CK level is elevated after exercise, then this indicates some muscle breakdown and strenuous exercise should be avoided until a diagnosis is made.
The combination of different systems affected - muscle, hearing, nerves could suggest a mitochondrial disorder. I am not sure what a 'single retinal spot' mean, but some mito disorder are associated with retinitis pigmentosa usually lots of spots on the retina, paricularly in the periphery of the retina - a full ophthalmological exam should be done, a bedside fundoscope is not enough as you cannot see the periphery. There are some specific genes for mitochondrial disease that can be tested on a blood sample, but the ordering doctor must know what is the more likely mitochondrial disorder before ordering them - a good pediatric neurologist should be able to tell you this.
The pediatric neuromuscular neurology department at the Cleveland Clinic (Dr. Neil Friedman) or another major center could help sort out the diagnosis if needed
I might be just throwing out something here, but this case sounds like a demyelination problem. There is a whole strain of them, and I do not know if there is a test available yet for them. Have they ruled out adrenoleukodystrophy? With the hearing problems and extreme muscle problems it may benefit to check out.
There are many muscle diseases, some mitochondrial, some not -- that can result in with various forms of exercise induced myopathies. You need to go to an experienced neuromuscular specialist or myologist who will order the right panel of tests -- unfortunately, another muscle biopsy may also be necessary.
Depending where you are, you can contact a major department's head of Neuromuscular diseases to suggest someone experienced in your area. Columbia in NYC has a specialist by the name of Salvatore DiMauro who could be of help.
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