Is there a minimum threshhold of genetic difference required for organ rejection to occur?
If, for example, scientists produce a cloned liver for an alcoholic ten years from now, and wanted to alter a single gene to make it more disease resistant, would the recipient’s body reject it because of the single-gene difference?
Since no one has bitten yet, let me offer a broad overivew in the hopes that someone more knowledgeable will fill in the details.
We (as do all mammals) have genes that encode for specific protiens which every cell uses to tell the immune system: Don’t attack me, I’m one of you! As long as you didn’t tinker with one of those genes, you’d be OK. There are quite a number of genes invovled in that process, though, so you’d have to be careful. But you should be able to add a gene to your cloned liver so that it, say, glows in the dark, but your immune system will still think it’s just regular ol’ you.
That’s helpful. Do you know the percentage of the whole that these marker genes represent? Is it theoretically possible that a donor organ, then, matches a recipient on those key markers? And has it happened? 
I believe a standard compatibility screening test looks at about 20ish antigens. I’d google “histocompatibility” or “major histocompatibility complex” for more information.
But back to your original question, unless the gene in question encodes a protein that is expressed on the cell surface (or would have a downstream affect on those proteins), it will more than likely not cause rejection. If it does affect cell surface proteins, you’d have to test to see how much of a reaction it would provoke.
Excellent. One less speedbump for my plans for immortality. Muhuhahaha!
Er… thanks!