A systematic survey of loss-of-function variants in human protein-coding genes

Daniel G. MacArthur, Suganthi Balasubramanian, Adam Frankish, Ni Huang, James Morris, Klaudia Walter, Luke Jostins, Lukas Habegger, Joseph K. Pickrell, Stephen B. Montgomery, Cornelis A. Albers, Zhengdong D. Zhang, Donald F. Conrad, Gerton Lunter, Hancheng Zheng, Qasim Ayub, Mark A. DePristo, Eric Banks, Min Hu, Robert E. HandsakerJeffrey A. Rosenfeld, Menachem Fromer, Mike Jin, Xinmeng Jasmine Mu, Ekta Khurana, Kai Ye, Mike Kay, Gary Ian Saunders, Marie Marthe Suner, Toby Hunt, If H.A. Barnes, Clara Amid, Denise R. Carvalho-Silva, Alexandra H. Bignell, Catherine Snow, Bryndis Yngvadottir, Suzannah Bumpstead, David N. Cooper, Yali Xue, Irene Gallego Romero, Jun Wang, Yingrui Li, Richard A. Gibbs, Steven A. McCarroll, Emmanouil T. Dermitzakis, Jonathan K. Pritchard, Jeffrey C. Barrett, Jennifer Harrow, Matthew E. Hurles, Mark B. Gerstein, Chris Tyler-Smith

Research output: Contribution to journalArticle

720 Scopus citations

Abstract

Genome-sequencing studies indicate that all humans carry many genetic variants predicted to cause loss of function (LoF) of protein-coding genes, suggesting unexpected redundancy in the human genome. Here we apply stringent filters to 2951 putative LoF variants obtained from 185 human genomes to determine their true prevalence and properties. We estimate that human genomes typically contain ∼100 genuine LoF variants with ∼20 genes completely inactivated. We identify rare and likely deleterious LoF alleles, including 26 known and 21 predicted severe disease-causing variants, as well as common LoF variants in nonessential genes. We describe functional and evolutionary differences between LoF-tolerant and recessive disease genes and a method for using these differences to prioritize candidate genes found in clinical sequencing studies.

Original languageEnglish (US)
Pages (from-to)823-828
Number of pages6
JournalScience
Volume335
Issue number6070
DOIs
StatePublished - Feb 17 2012

ASJC Scopus subject areas

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    MacArthur, D. G., Balasubramanian, S., Frankish, A., Huang, N., Morris, J., Walter, K., Jostins, L., Habegger, L., Pickrell, J. K., Montgomery, S. B., Albers, C. A., Zhang, Z. D., Conrad, D. F., Lunter, G., Zheng, H., Ayub, Q., DePristo, M. A., Banks, E., Hu, M., ... Tyler-Smith, C. (2012). A systematic survey of loss-of-function variants in human protein-coding genes. Science, 335(6070), 823-828. https://doi.org/10.1126/science.1215040