A snapshot of some pLI score pitfalls

Hum Mutat. 2019 Jul;40(7):839-841. doi: 10.1002/humu.23763. Epub 2019 Apr 29.

Abstract

The pLI score reflects the tolerance of a given gene to the loss of function on the basis of the number of protein truncating variants, that is, the frameshift, splice donor, splice acceptor, and stop-gain variants referenced for this gene in control databases weighted by the size of the gene and the sequencing coverage. It is frequently used to prioritize candidate genes when analyzing whole exome or whole genome data. We list here the main pitfalls to consider before using this score. Concrete illustrations are given for each of these pitfalls.

Keywords: exome sequencing analysis; loss of function; pLI score.

MeSH terms

  • Codon, Nonsense
  • Computational Biology / methods*
  • Exome Sequencing
  • Frameshift Mutation
  • Humans
  • Loss of Function Mutation*
  • Mutation, Missense
  • Proteins / genetics*
  • RNA Splice Sites
  • Sequence Analysis, DNA / methods*
  • Whole Genome Sequencing

Substances

  • Codon, Nonsense
  • Proteins
  • RNA Splice Sites