In analyses with the LINKAGE programs one can define liability classes. Subjects within the same liability class share the same sets of penetrance values, but these can differ between liability classes. For example, if liability classes are defined in terms of age then sets of penetrance values may vary according to age. Other factors which could be used to define liability classes include sex, exposure to environmental risk factors, geography, ethnicity.
For factors such as age and sex the frequency of the abnormal allele will usually be constant across liability classes, with just the penetrance values varying, but not the freqency of the abnormal allele.