What if you don’t know which allele is mutant? For example, what if you’re presented with two true-breeding frogs: one that is gold and one that is yellow. If you don’t know what the predominant colour in nature is you can’t know which one is mutant. If you crossed them and all the progeny are gold, then you know the dominant allele encodes a protein to make it gold. The recessive, therefore, is “yellow” and you should name the gene “y” after the recessive phenotype. This means the dominant allele would be “Y”. Your offspring would therefore be Yy and the gold parent would be YY. The yellow parent would be yy. 
Figure 2 from the Appendix shows purple and white flowers. . If we note the genotypes, we can see that the het (middle) shows the same colour as the purple parent; thus purple is dominant. "Albino" is a good name for the white mutant phenotype, so let's call the recessive allele a.
This means that the wild-type allele, which is dominant, would be indicated as A.
This means that the gene NAME is albino, and in our system there are two alleles for the albino gene; the mutant allele, causing albinism, and the wild-type, which allows normal colour.
Let’s always choose a letter based on the mutant phenotype for our gene symbol. If we are presented with a ladybug mutant that is small, we might choose “d” for “dwarf”. Geneticists sometimes set up a research program based on unusual phenotypes of the organism they are studying. The fact that a mutant phenotype that is heritable exists tells us that there is a genetic control for the trait and that it might be isolated in the lab. When you look at your classmates, you don’t necessarily note that none of them has an arm growing from the tops of their heads. If one student had this trait, however, you couldn’t help but notice it. If you found out it showed up in that student’s ancestry in a predictable fashion, you might reasonably suggest that there is a genetic basis for that. If it happened to be controlled by a single gene, you might call the gene “extra arm” or “arm head”. If it happened to be a dominant trait, you might use the letter “X” (for “Xtra”) or “A” (for “Arm) for the mutant allele. The wild type allele would be “x” or “a”, respectively.
When you’re writing down gene symbols for homework or on an exam, be sure to make the characters distinct. A typewritten “y” is easy to distinguish from the upper case “Y” but not as easy when writing it down. Instructors who ask you to show your work need to be able to follow your logic train. More important than that is YOU have to be able to follow your own reasoning. Students often switch symbols and come up with an answer that is inconsistent with the data given because of this. Consider underlining your capitals or putting a line through one of them to make it distinct (e.g. Y for the dominant allele; y for the recessive).
There are many ways to name genes. The first rule is that both the wild-type and mutant, or dominant and recessive, must be identifiably linked to each other. For example, if you're looking at a curly-haired mutation, the allele responsible could be called "c" for curly, and the wild-type allele could be called "C". Hint: be sure that hand-written symbols are distinct!
This module shows a simple single-letter method of naming genes.