The question is ambiguous, in my opinion it deals in non-absolutes (we need more info). I can't see any reason why, when you mention the word "gene" in general, you wouldn't be talking about phenotype in some way, on some level. Gene's which do not alter the appearance of an organism- I'd say that doesn't really exist. You can rule out what the human eye cannot detect, or else somebody is going to "see" different genes when they look at the gene itself, so it depends on how closely we "look" at an organism. Phenotype as an expression of what you can and cannot see? Molecular biology would impact both. Epigenetics is heritable and alters genes in other ways besides directly (histone modifications) so this would be my choice overall if guessing on a test. I feel as though, there is no right answer to a question like this. And I am sure as times change the answer will likely vary and new terms for genetic approaches will be developed, so it depends on the year in which we ask ourselves these questions.
