PreprintCited by 354Genomics and Rare DiseasesGenetic Associations and EpidemiologyGenomics and Phylogenetic Studies

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Regional missense constraint improves variant deleteriousness prediction

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Samocha, Kaitlin E., Kosmicki, Jack A., Karczewski, Konrad J., O’Donnell-Luria, Anne H., Pierce-Hoffman, Emma, MacArthur, Daniel G., Neale, Benjamin M., Daly, Mark J.·2017·bioRxiv (Cold Spring Harbor Laboratory)

Abstract

Given increasing numbers of patients who are undergoing exome or genome sequencing, it is critical to establish tools and methods to interpret the impact of genetic variation. While the ability to predict deleteriousness for any given variant is limited, missense variants remain a particularly challenging class of variation to interpret, since they can have drastically different effects depending on both the precise location and specific amino acid substitution of the variant. In order to better evaluate missense variation, we leveraged the exome sequencing data of 60,706 individuals from the Exome Aggregation Consortium (ExAC) dataset to identify sub-genic regions that are depleted of missense variation. We further used this depletion as part of a novel missense deleteriousness metric named MPC. We applied MPC to de novo missense variants and identified a category of de novo missense variants with the same impact on neurodevelopmental disorders as truncating mutations in intolerant genes, supporting the value of incorporating regional missense constraint in variant interpretation.

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  1. 10.1093/bioinformatics/btq330 · DOI
  2. 10.1093/bioinformatics/btv112 · DOI

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Metadata

Authors
Samocha, K. E., Kosmicki, J. A., Karczewski, K. J., O’Donnell-Luria, A. H., Pierce-Hoffman, E., MacArthur, D. G., Neale, B. M., & Daly, M. J.
Affiliations
Broad Institute (US)
Corresponding author
Daly, Mark J.
Venue
bioRxiv (Cold Spring Harbor Laboratory)
Publisher
openRxiv
Published
2017-06-12
OpenAlex
W2625862723
Cited by
351
References
28
Citations by year
2026: 19 · 2025: 42 · 2024: 56 · 2023: 43 · 2022: 47 · 2021: 49 · 2020: 34 · 2019: 40 · 2018: 17 · 2017: 3
Type
posted content
Language
en
Open access
Locations
bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
Funders
National Institute of General Medical Sciences (F32GM115208, T32GM007748)
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 › Molecular Biology › Genomics and Phylogenetic Studies
Keywords
missense mutations, variant interpretation, de novo mutations, neurodevelopmental disorders, ExAC, truncating mutations

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