We know enough to know that stop codon stops the transcription of the gene before the protein it codes for is produced. We aren't (as you point out) omnicient, but that is plenty of knowledge to safely conclude that this gene no longer functions. The burden of proof now shifts to the person who claims that there is some "hidden" function for this gene - to show that it does indeed have that function and that its function requires this particular sequence and no other. Else the claim "common designer" does not explain the homology between this gene in humans and chimps. It really is that simple, no matter how loud you shout, or how hard you wave your hands.
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