the mutations are in cis in the same gene, the diploid organism has one wild type and one doubly-mutated copy of that gene, but when the mutations in the same gene are in trans, the organism has no wild type copies of the gene, and the phenotype may not be the same. Cis-trans tests can reveal allelism between dominant and recessive mutations, and they can distinguish allelism from non-allelic non-complementation.

Cis-trans test can also yield exceptions. For example, the cis and trans combinations of the Drosophila mutations Cbx¹