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The Characteristics of Heterozygous Protein Truncating Variants in the Human Genome.

Type of publication Peer-reviewed
Publikationsform Original article (peer-reviewed)
Author Bartha István, Rausell Antonio, McLaren Paul J, Mohammadi Pejman, Tardaguila Manuel, Chaturvedi Nimisha, Fellay Jacques, Telenti Amalio,
Project Swiss HIV Cohort Study (SHCS)
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Original article (peer-reviewed)

Journal PLoS computational biology
Volume (Issue) 11(12)
Page(s) 1004647 - 1004647
Title of proceedings PLoS computational biology
DOI 10.1371/journal.pcbi.1004647

Open Access

Type of Open Access Publisher (Gold Open Access)


Sequencing projects have identified large numbers of rare stop-gain and frameshift variants in the human genome. As most of these are observed in the heterozygous state, they test a gene's tolerance to haploinsufficiency and dominant loss of function. We analyzed the distribution of truncating variants across 16,260 autosomal protein coding genes in 11,546 individuals. We observed 39,893 truncating variants affecting 12,062 genes, which significantly differed from an expectation of 12,916 genes under a model of neutral de novo mutation (p<10-4). Extrapolating this to increasing numbers of sequenced individuals, we estimate that 10.8% of human genes do not tolerate heterozygous truncating variants. An additional 10 to 15% of truncated genes may be rescued by incomplete penetrance or compensatory mutations, or because the truncating variants are of limited functional impact. The study of protein truncating variants delineates the essential genome and, more generally, identifies rare heterozygous variants as an unexplored source of diversity of phenotypic traits and diseases.