First of all, I am glad you have a dr that is looking into this so thoroughly. Your son clearly needs this, no matter what's going on with him. All too often we see drs that brush off a severe dx and then a parent is left with a child that is STILL very ill and left with no tools with which to deal with it! My daughter has one known mutation (df508, the most common one) and one unknown mutation. She too had the Ambry Amplified w/deletions & duplications, the most comprehensive testing out there for CF. Having NO known mutations is very rare, but not impossible. As Steve (our resident expert here on their testing) tells us, there is NO genetic test that can 100% rule out this disease. Diagnosis is an art and not all drs are equally open-minded here- you must combine genetic testing, the sweat test, results of newborn screening (when applicable), symptoms, test results (sputum cultures, xrays/ct scans, etc), and response to treatment when forming a diagnosis.
There is a genetic test for SDS so it makes sense to rule it out. It's uncommon to have elevated sweat tests with that but it does happen in some cases. Since other health conditions are common with that syndrome, identifying it would be important. (If he has no sign of other symptoms commonly seen with it, your son's dr may have already thought of it and discarded it.) With Primary Ciliary Diskinesia, genetic testing can identify it in some cases and in many others, analyzing the cilia in the respiratory tract can diagnose it so that makes sense as well to at least look into and rule out. That disease presents VERY much like CF (and is treated very much like it as well.)
I agree with doing some form of airway clearance and nebs daily to see if that helps. <img src="i/expressions/face-icon-small-smile.gif" border="0"> I wish you and your son the best- welcome to the site!