Identification of a large set of rare complete human knockouts
Abstract
Loss-of-function mutations cause many mendelian diseases. Here we aimed to create a catalog of autosomal genes that are completely knocked out in humans by rare loss-of-function mutations. We sequenced the whole genomes of 2,636 Icelanders and imputed the sequence variants identified in this set into 101,584 additional chip-genotyped and phased Icelanders. We found a total of 6,795 autosomal loss-of-function SNPs and indels in 4,924 genes. Of the genotyped Icelanders, 7.7% are homozygotes or compound heterozygotes for loss-of-function mutations with a minor allele frequency (MAF) below 2% in 1,171 genes (complete knockouts). Genes that are highly expressed in the brain are less often completely knocked out than other genes. Homozygous loss-of-function offspring of two heterozygous parents occurred less frequently than expected (deficit of 136 per 10,000 transmissions for variants with MAF <2%, 95% confidence interval (CI) = 10-261).
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The observed deficit (13.7%) is higher than the 6.4% deficit reported in the Icelandic population.
“This deficit is higher than in the Icelandic population (6.4%)(3)”
From Health and population effects of rare gene knockouts in adult humans with related parents (2016) · cites this paper as [3]
1,171 genes with complete predicted loss-of-function were identified in 104,220 Icelandic individuals.
“Furthermore, 1,171 genes with complete predicted LOF were identified in 104,220 Icelandic individuals (3)”
From Health and population effects of rare gene knockouts in adult humans with related parents (2016) · cites this paper as [3]
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Less Is More, Natural Loss-of-Function Mutation Is a Strategy for Adaptation
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Compound heterozygous mutations in UBA5 causing early-onset epileptic encephalopathy in two sisters
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From lipid locus to drug target through human genomics
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- Authors
- Sulem, P., Helgason, H., Oddson, A., Stefansson, H., Gudjonsson, S. A., Zink, F., Hjartarson, E., Sigurdsson, G. T., Jonasdottir, A., Jonasdottir, A., Sigurdsson, A., Magnusson, O. T., Kong, A., Helgason, A., Holm, H., Thorsteinsdottir, U., Masson, G., Gudbjartsson, D. F., & Stefansson, K.
- Affiliations
- deCODE Genetics (Iceland) (IS)
- Corresponding author
- Sulem, Patrick
- Venue
- Nature Genetics
- Published
- 2015-03-25
- Volume
- 47
- Issue
- 5
- Pages
- 448-452
- ISSN
- 1061-4036 (ISSN-L)
- 1546-1718
- OpenAlex
- W2078889486
- Cited by
- 220
- References
- 37
- Citations by year
- 2026: 5 · 2025: 14 · 2024: 10 · 2023: 13 · 2022: 14 · 2021: 10 · 2020: 15 · 2019: 24 · 2018: 22 · 2017: 36 · 2016: 35 · 2015: 22
- FWCI
- 26.69
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Genetics (publishedVersion)
- PubMed (publishedVersion)
- Hirsla (Landspítali University Hospital) (submittedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Keywords
- loss-of-function mutations, homozygous mutation, compound heterozygosity, rare variants, monogenic disorders, autosomal genes, brain gene expression, Icelandic population
- MeSH terms
- Brain, Female, Gene Frequency, Heterozygote, Homozygote, Humans, Male, Organ Specificity, Gene Expression, Genome, Human, Open Reading Frames, Sequence Analysis, DNA, Polymorphism, Single Nucleotide, INDEL Mutation, Gene Ontology
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