Can we detect or guess or estimate phenocopies computationally?

Question

[Sharon]

Hi Everyone

Is there a way to detect phenocopies -computationally-, like could linkage analysis help or any other method I am oblivious of? We have an interesting variant x segregating in all affected from gene G. But for one patient we have variant y from the same gene but not x. I was thinking if there is a possibility that this patient is a phenocopy. But I lack any hint/thought on how to track this hypothesis down, is it even a reasonable assumption?

Thanks