For an "affection-status" locus, each genotype has an associated penetrance; this is the probability that an individual with a particular genotype will be affected. Penetrance can also be defined as a function of liability classes. In this case, one penetrance is given for each genotype in each liability class. The classes are numbered sequentially starting from 1. With two or more liability classes, the phenotype is the affection status plus the class number. When a single affection status class is defined, the class number is not included as part of the phenotype.
With sex-linked traits, different penetrances must be given for females and males. One penetrance in males is specified for each allele in each liability class.