Measuring “Intolerance to Mutation” in Human Genetics

In numerous applications, from working with animal models to mapping the genetic basis of human disease susceptibility, it is useful to know whether a single disrupting mutation in a gene is likely to be deleterious 1–4 . With this goal in mind, a number of measures have been developed to identify genes in which protein-truncating variants (PTVs), or other types of mutations, are absent or kept at very low frequency in large population samples—genes that appear “intolerant to mutation” 3,5–9 . One measure in particular, pLI, has been widely adopted 7 . By contrasting the observed versus expected number of PTVs, it aims to classify genes into three categories, labelled “null”, “recessive” and “haploinsufficient” 7 . Such population genetic approaches can be useful in many applications. As we clarify, however, these measures reflect the strength of selection acting on heterozygotes, and not dominance for fitness or haploinsufficiency for other phenotypes.