Refining the role of de novo protein-truncating variants in neurodevelopmental disorders by using population reference samples
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Abstract
Recent research has uncovered an important role for de novo variation in neurodevelopmental disorders. Using aggregated data from 9,246 families with autism spectrum disorder, intellectual disability, or developmental delay, we found that ∼1/3 of de novo variants are independently present as standing variation in the Exome Aggregation Consortium's cohort of 60,706 adults, and these de novo variants do not contribute to neurodevelopmental risk. We further used a loss-of-function (LoF)-intolerance metric, pLI, to identify a subset of LoF-intolerant genes containing the observed signal of associated de novo protein-truncating variants (PTVs) in neurodevelopmental disorders. LoF-intolerant genes also carry a modest excess of inherited PTVs, although the strongest de novo-affected genes contribute little to this excess, thus suggesting that the excess of inherited risk resides in lower-penetrant genes. These findings illustrate the importance of population-based reference cohorts for the interpretation of candidate pathogenic variants, even for analyses of complex diseases and de novo variation.
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Autistic females are more likely to have high-impact de novo variants than autistic males.
“Autistic females are more likely to have high-impact de novo variants than autistic males17,26,46,47”
From Genetic correlates of phenotypic heterogeneity in autism (2022) · cites this paper as [26]
Rare inherited LGD variants in constrained genes confer increased risk for ASD.
“These results provide further evidence that rare, inherited LGD variants in constrained genes confer increased risk for ASD.14,15”
From Exome sequencing of 457 autism families recruited online provides evidence for autism risk genes (2019) · cites this paper as [15]
Existing methods for detecting gene-specific enrichment of damaging de novo mutations ignore much prior information about which variants are more likely disease-associated.
“Existing methods to detect gene-specific enrichments of damaging DNMs ignore much prior information about which variants are more likely to be disease-associated; missense variants and protein-truncating variants (PTVs) vary in their impact on protein function3–6.”
From Evidence for 28 genetic disorders discovered by combining healthcare and research data (2020) · cites this paper as [5]
Missense variants and protein-truncating variants differ in their impact on protein function.
“missense variants and protein-truncating variants (PTVs) vary in their impact on protein function3–6.”
From Evidence for 28 genetic disorders discovered by combining healthcare and research data (2020) · cites this paper as [5]
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- [35]Large-scale discovery of novel genetic causes of developmental disorders Nature 519 223 8 2015 25533962 PMC5955210
- [36]Lek M Analysis of protein-coding genetic variation in 60,706 humans bioRxiv 2015 PMC5018207 27535533
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Self-citation
- Authors
- Kosmicki, J. A., Samocha, K. E., Howrigan, D. P., Sanders, S. J., Slowikowski, K., Lek, M., Karczewski, K. J., Cutler, D. J., Devlin, B., Roeder, K., Buxbaum, J. D., Neale, B. M., MacArthur, D. G., Wall, D. P., Robinson, E. B., & Daly, M. J.
- Affiliations
- Broad Institute (US)
- University of California, San Francisco (US)
- Emory University (US)
- University of Pittsburgh (US)
- Carnegie Mellon University (US)
- Icahn School of Medicine at Mount Sinai (US)
- Stanford Medicine (US)
- Corresponding author
- Daly, Mark J
- ORCID
- Venue
- Nature Genetics
- Published
- 2017-02-13
- Volume
- 49
- Issue
- 4
- Pages
- 504-510
- ISSN
- 1061-4036 (ISSN-L)
- 1546-1718
- PMC
- PMC5496244
- OpenAlex
- W2949181286
- Cited by
- 340
- References
- 48
- Citations by year
- 2026: 12 · 2025: 20 · 2024: 35 · 2023: 22 · 2022: 34 · 2021: 38 · 2020: 46 · 2019: 54 · 2018: 45 · 2017: 34
- FWCI
- 32.49
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Licence
- cc-by-nd
- www.springer.com/tdm (tdm)
- Locations
- Nature Genetics (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nd)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- Simons Foundation (SFARI 342292)
- National Alliance for Research on Schizophrenia and Depression
- Simons Foundation Autism Research Initiative
- National Institutes of Health (5k01mh099286-02, T32 HG002295/HG/NHGRI)
- Simons Center for the Social Brain, Massachusetts Institute of Technology
- National Institute of Mental Health (U01MH100209, U01MH111661, U01MH100229, R01MH097849, U01MH111658, U01MH100239, R56MH097849, K01 MH099286, U01MH111660, U01MH100233)
- National Human Genome Research Institute (T32 HG002295/HG/NHGRI, HG002295, T32HG002295)
- National Institute of General Medical Sciences (R01GM104371)
- National Institute of Diabetes and Digestive and Kidney Diseases (U54DK105566)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetics and Neurodevelopmental Disorders
- Life Sciences › Neuroscience › Cognitive Neuroscience › Autism Spectrum Disorder Research
- Keywords
- neurodevelopmental disorders, autism spectrum disorder, intellectual disability, developmental delay, loss-of-function intolerance, ExAC, inherited mutations, genetic risk
- MeSH terms
- Autism Spectrum Disorder, Humans, Intellectual Disability, Phenotype, Genetic Variation, Genetic Predisposition to Disease, Exome, Neurodevelopmental Disorders
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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