title: The Characteristics of Heterozygous Protein Truncating Variants in the Human Genome.
abstract: 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.
authors.affiliation: SIB Swiss Institute of Bioinformatics, Lausanne and Basel, Switzerland.|School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
authors.forename: István
authors.initials: I
authors.lastname: Bartha
authors.affiliation: SIB Swiss Institute of Bioinformatics, Lausanne and Basel, Switzerland.|Vital-IT group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.
authors.forename: Antonio
authors.initials: A
authors.lastname: Rausell
authors.affiliation: SIB Swiss Institute of Bioinformatics, Lausanne and Basel, Switzerland.|School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
authors.forename: Paul J
authors.initials: PJ
authors.lastname: McLaren
authors.affiliation: SIB Swiss Institute of Bioinformatics, Lausanne and Basel, Switzerland.|Computational Biology Group, ETH Zurich, Zurich, Switzerland.
authors.forename: Pejman
authors.initials: P
authors.lastname: Mohammadi
authors.affiliation: SIB Swiss Institute of Bioinformatics, Lausanne and Basel, Switzerland.|Vital-IT group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.
authors.forename: Manuel
authors.initials: M
authors.lastname: Tardaguila
authors.affiliation: SIB Swiss Institute of Bioinformatics, Lausanne and Basel, Switzerland.|School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
authors.forename: Nimisha
authors.initials: N
authors.lastname: Chaturvedi
authors.affiliation: SIB Swiss Institute of Bioinformatics, Lausanne and Basel, Switzerland.|School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
authors.forename: Jacques
authors.initials: J
authors.lastname: Fellay
authors.affiliation: J. Craig Venter Institute, La Jolla, California, United States of America.
authors.forename: Amalio
authors.initials: A
authors.lastname: Telenti
mesh_terms: D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D018389:Codon, Nonsense / Q000235:genetics*; D014644:Genetic Variation / Q000235:genetics*; D015894:Genome, Human / Q000235:genetics*; D006801:Humans; D008969:Molecular Sequence Data; D011506:Proteins / Q000235:genetics*
chemical_list: D018389:Codon, Nonsense; D011506:Proteins