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Effect of predicted protein-truncating genetic variants on the human transcriptome
Open accessAbstract
Expression, genetic variation, and tissues: Human genomes show extensive genetic variation across individuals, but we have only just started documenting the effects of this variation on the regulation of gene expression. Furthermore, only a few tissues have been examined per genetic variant. In order to examine how genetic expression varies among tissues within individuals, the Genotype-Tissue Expression (GTEx) Consortium collected 1641 postmortem samples covering 54 body sites from 175 individuals. They identified quantitative genetic traits that affect gene expression and determined which of these exhibit tissue-specific expression patterns. Melé et al. measured how transcription varies among tissues, and Rivas et al. looked at how truncated protein variants affect expression across tissues. Science , this issue p. 648 , p. 660 , p. 666 ; see also p. 640
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“Furthermore, protein-truncating variants (PTVs) are among the most interpretable associations as they suggest that the effect on disease most commonly tracks with decreasing expression of the gene 15 .”
From Exome sequencing identifies rare coding variants in 10 genes which confer substantial risk for schizophrenia (2020) · cites this paper as [15]
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“The most natural grouping for rare variants is within a gene, based on predicted functional consequence or evidence for deleteriousness16,17.”
From Rare coding variants in ten genes confer substantial risk for schizophrenia (2022) · cites this paper as [17]
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Xu, J., Schmidt, J., Campbell, A., Bozkurt‐Yozgatli, T., Egab, I., Mestroni, L., Taylor, M., Posey, J. E., Gibbs, R. A., Boerwinkle, E., et al. (2025) · medRxiv · doi:10.64898/2025.12.01.25341387
Sherbina, K., León-Novelo, L. G., Nuzhdin, S. V., McIntyre, L. M., & Marroni, F. (2021) · Figshare · doi:10.6084/m9.figshare.17087885
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Sun, B., & Chen, L. (2023) · Figshare · doi:10.6084/m9.figshare.23665377
Sherbina, K., León-Novelo, L. G., Nuzhdin, S. V., McIntyre, L. M., & Marroni, F. (2021) · Figshare · doi:10.6084/m9.figshare.17087882
Blakes, A. J. M., Wai, H. A., Davies, I., Moledina, H. E., Ruiz, A., Thomas, T., Bunyan, D. J., Thomas, N. S., Burren, C. P., Greenhalgh, L., et al. (2022) · Figshare · doi:10.6084/m9.figshare.20381694
Topa, H., Benoit‐Pilven, C., Tukiainen, T., & Pietiläinen, O. (2024) · Figshare · doi:10.6084/m9.figshare.26728381
Self-citationSun, B., & Chen, L. (2023) · Figshare · doi:10.6084/m9.figshare.23665395
Additional file 4 of A vast resource of allelic expression data spanning human tissues
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Self-citationAdditional file 3 of Nanopore sequencing reveals endogenous NMD-targeted isoforms in human cells
Karousis, E. D., Gypas, F., Zavolan, M., & Mühlemann, O. (2021) · Figshare · doi:10.6084/m9.figshare.15178689
Sherbina, K., León-Novelo, L. G., Nuzhdin, S. V., McIntyre, L. M., & Marroni, F. (2021) · Figshare · doi:10.6084/m9.figshare.17087891
Topa, H., Benoit‐Pilven, C., Tukiainen, T., & Pietiläinen, O. (2024) · Figshare · doi:10.6084/m9.figshare.25951968
Self-citation
Metadata
- Authors
- Rivas, M. A., Pirinen, M., Conrad, D. F., Lek, M., Tsang, E. K., Karczewski, K. J., Maller, J. B., Kukurba, K. R., DeLuca, D. S., Fromer, M., Ferreira, P. G., Smith, K. S., Zhang, R., Zhao, F., Banks, E., Poplin, R., Ruderfer, D. M., Purcell, S. M., Tukiainen, T., Minikel, E. V., Stenson, P. D., Cooper, D. N., Huang, K. H., Sullivan, T. J., Nedzel, J., The GTEx Consortium, The Geuvadis Consortium, Bustamante, C. D., Li, J. B., Daly, M. J., Guigo, R., Donnelly, P., Ardlie, K., Sammeth, M., Dermitzakis, E. T., McCarthy, M. I., Montgomery, S. B., Lappalainen, T., MacArthur, D. G., Segre, A. V., Young, T. R., Gelfand, E. T., Trowbridge, C. A., Ward, L. D., Kheradpour, P., Iriarte, B., Meng, Y., Palmer, C. D., Esko, T., Winckler, W., Hirschhorn, J., Kellis, M., Getz, G., Shablin, A. A., Li, G., Zhou, Y.-H., Nobel, A. B., Rusyn, I., Wright, F. A., Battle, A., Mostafavi, S., Mele, M., Reverter, F., Goldmann, J., Koller, D., Gamazon, E. R., Im, H. K., Konkashbaev, A., Nicolae, D. L., Cox, N. J., Flutre, T., Wen, X., Stephens, M., Pritchard, J. K., Tu, Z., Zhang, B., Huang, T., Long, Q., Lin, L., Yang, J., Zhu, J., Liu, J., Brown, A., Mestichelli, B., Tidwell, D., Lo, E., Salvatore, M., Shad, S., Thomas, J. A., Lonsdale, J. T., Choi, R. C., Karasik, E., Ramsey, K., Moser, M. T., Foster, B. A., Gillard, B. M., Syron, J., Fleming, J., Magazine, H., Hasz, R., Walters, G. D., Bridge, J. P., Miklos, M., Sullivan, S., Barker, L. K., Traino, H., Mosavel, M., Siminoff, L. A., Valley, D. R., Rohrer, D. C., Jewel, S., Branton, P., Sobin, L. H., Barcus, M., Qi, L., Hariharan, P., Wu, S., Tabor, D., Shive, C., Smith, A. M., Buia, S. A., Undale, A. H., Robinson, K. L., Roche, N., Valentino, K. M., Britton, A., Burges, R., Bradbury, D., Hambright, K. W., Seleski, J., Korzeniewski, G. E., Erickson, K., Marcus, Y., Tejada, J., Taherian, M., Lu, C., Robles, B. E., Basile, M., Mash, D. C., Volpi, S., Struewing, J. P., Temple, G. F., Boyer, J., Colantuoni, D., Little, R., Koester, S., Carithers, L. J., Moore, H. M., Guan, P., Compton, C., Sawyer, S. J., Demchok, J. P., Vaught, J. B., Rabiner, C. A., Lockhart, N. C., Friedlander, M. R., ’t Hoen, P. A. C., Monlong, J., Gonzàlez-Porta, M., Kurbatova, N., Griebel, T., Barann, M., Wieland, T., Greger, L., van Iterson, M., Almlof, J., Ribeca, P., Pulyakhina, I., Esser, D., Giger, T., Tikhonov, A., Sultan, M., Bertier, G., Lizano, E., Buermans, H. P. J., Padioleau, I., Schwarzmayr, T., Karlberg, O., Ongen, H., Kilpinen, H., Beltran, S., Gut, M., Kahlem, K., Amstislavskiy, V., Stegle, O., Flicek, P., Strom, T. M., Lehrach, H., Schreiber, S., Sudbrak, R., Carracedo, A., Antonarakis, S. E., Hasler, R., Syvanen, A.-C., van Ommen, G.-J., Brazma, A., Meitinger, T., Rosenstiel, P., Gut, I. G., & Estivill, X.
- Affiliations
- Centre for Human Genetics (GB)
- University of Helsinki (FI)
- Washington University in St. Louis (US)
- Broad Institute (US)
- Stanford Medicine (US)
- University of Geneva (CH)
- Stanford University (US)
- Mount Sinai Hospital (US)
- Cardiff University (GB)
- Center for Genomic Regulation (CRG), Universitat Pompeu Fabra (UPF), Barcelona, Catalonia, Spain.
- Universitat Pompeu Fabra (ES)
- Corresponding author
- Rivas, Manuel A.
- Pirinen, Matti
- Conrad, Donald F.
- Lek, Monkol
- Lappalainen, Tuuli
- MacArthur, Daniel G.
- ORCID
- Rivas, Manuel A.
- Pirinen, Matti
- Conrad, Donald F.
- Lek, Monkol
- Tsang, Emily K.
- Karczewski, Konrad J.
- Maller, Julian B.
- DeLuca, David S.
- Fromer, Menachem
- Ferreira, Pedro G.
- Smith, Kevin S.
- Zhang, Rui
- Zhao, Fengmei
- Banks, Eric
- Ruderfer, Douglas M.
- Purcell, Shaun M.
- Tukiainen, Taru
- Minikel, Eric V.
- Cooper, David N.
- Nedzel, Jared
- Bustamante, Carlos D.
- Li, Jin Billy
- Daly, Mark J.
- Donnelly, Peter
- Ardlie, Kristin
- Sammeth, Michael
- Dermitzakis, Emmanouil T.
- McCarthy, Mark I.
- Montgomery, Stephen B.
- Lappalainen, Tuuli
- MacArthur, Daniel G.
- Young, Taylor R.
- Ward, Lucas D.
- Meng, Yan
- Palmer, Cameron D.
- Winckler, Wendy
- Hirschhorn, Joel
- Kellis, Manolis
- Getz, Gad
- Li, Gen
- Zhou, Yi-Hui
- Nobel, Andrew B.
- Rusyn, Ivan
- Wright, Fred A.
- Battle, Alexis
- Mostafavi, Sara
- Goldmann, Jakob
- Koller, Daphne
- Gamazon, Eric R.
- Im, Hae Kyung
- Konkashbaev, Anuar
- Nicolae, Dan L.
- Cox, Nancy J.
- Wen, Xiaoquan
- Stephens, Matthew
- Pritchard, Jonathan K.
- Tu, Zhidong
- Huang, Tao
- Long, Quan
- Lin, Luan
- Yang, Jialiang
- Zhu, Jun
- Moser, Michael T.
- Foster, Barbara A.
- Gillard, Bryan M.
- Siminoff, Laura A.
- Rohrer, Daniel C.
- Branton, Philip
- Tabor, David
- Lu, Chunrong
- Mash, Deborah C.
- Volpi, Simona
- Struewing, Jeffery P.
- Moore, Helen M.
- Guan, Ping
- Compton, Carolyn
- Sawyer, Sherilyn J.
- Monlong, Jean
- Gonzàlez-Porta, Mar
- Kurbatova, Natalja
- Griebel, Thasso
- Barann, Matthias
- Wieland, Thomas
- Greger, Liliana
- Ribeca, Paolo
- Sultan, Marc
- Bertier, Gabrielle
- Lizano, Esther
- Ongen, Halit
- Kilpinen, Helena
- Amstislavskiy, Vyacheslav
- Stegle, Oliver
- Flicek, Paul
- Schreiber, Stefan
- Sudbrak, Ralf
- Antonarakis, Stylianos E.
- Meitinger, Thomas
- Rosenstiel, Philip
- Gut, Ivo G.
- Estivill, Xavier
- Venue
- Science
- Published
- 2015-05-08
- Volume
- 348
- Issue
- 6235
- Pages
- 666-669
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- PMC
- PMC4537935
- OpenAlex
- W1843990841
- Cited by
- 313
- References
- 55
- Citations by year
- 2026: 15 · 2025: 24 · 2024: 28 · 2023: 36 · 2022: 25 · 2021: 34 · 2020: 25 · 2019: 23 · 2018: 24 · 2017: 30 · 2016: 33 · 2015: 16
- FWCI
- 23.60
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- Archive ouverte UNIGE (University of Geneva) (publishedVersion)
- PubMed Central (acceptedVersion)
- Data Archiving and Networked Services (DANS) (submittedVersion)
- Leiden Repository (Leiden University) (submittedVersion)
- UCL Discovery (University College London) (submittedVersion)
- ORCA Online Research @Cardiff (Cardiff University) (submittedVersion)
- Archive ouverte UNIGE (University of Geneva) (submittedVersion, cc-by)
- Funders
- National Institutes of Health (NIGMS R01GM104371, NIMH R01MH101814, R01MH090941, U01HG007593, R01MH101810)
- United States Department of Defense
- Wellcome Trust (095552/Z/11/Z, 090532/Z/09/Z, 98381)
- European Research Council
- Natural Science and Engineering Research Council of Canada
- University of Oxford
- Louis-Jeantet Foundation
- Swiss National Science Foundation
- Academy of Finland (257654)
- Clarendon Scholarship
- NDM Studentship
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Keywords
- truncating mutations, nonsense mutation, variant effect prediction, transcriptome, splice junctions, tissue-specific effects, position effect, dosage compensation, GTEx, GEUVADIS
- MeSH terms
- Gene Expression Regulation, Heterozygote, Humans, Phenotype, Proteins, Genetic Variation, Genome, Human, Alternative Splicing, Gene Silencing, Gene Expression Profiling, Nonsense Mediated mRNA Decay, Transcriptome
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