They're definitely on there. The questions I had mostly required that you know that a particular syndrome was a lysosomal storage disorder, but I've heard of others who had more specific questions about it. Definitely something to look over again quickly before the exam.
Its a good bet youll get at least one...but then of course, when you do only get one you will be pissed because you had to memorize them all and youll feel like you should be getting at least 3 or 4 points out of them. But that is just the nature of this beast.
I think I had two of them. You'll probably encounter them because they produce distinct syndromes and are therefore easily tested. Same goes for the glycogen storage diseases.
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