If the sentence in question had simply said
This disorder prevents the body from making a particular protein, or causes it to produce abnormal proteins.
you might argue that the comma is superfluous because the sentence's parallel structure is immediately evident to readers and amounts to
This disorder (1) prevents the body from making a particular protein or (2) causes it to produce abnormal proteins.
But as Janus Bahs Jacquet observes in a comment above, the fact that a comma isn't mandatory in a parallel construction like this one doesn't mean that including one is wrong. I don't deny that a comma may sometimes act as a needless (though very minor) impediment to brisk reading, as here:
My father eats pretzels, and drinks beer.
but I don't think that the comma in my shortened version of your original sentence has that hindering effect, and I certainly don't think that the comma in the original sentence does. If anything, it usefully marks where the second branch of the parallel structure begins.
None of this discussion is related to comma splices—because, as FumbleFingers observes in a comment above, the comma in your original sentence doesn't create a comma splice. If it had done so, you'd have been able to confirm that fact by setting up the clause after the comma as a separate sentence and seeing that it was complete. Since
Causes it to be made in an abnormal form.
doesn't work as a complete sentence, there is no comma-splice issue here.