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A genomic mutational constraint map using variation in 76,156 human genomes
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Abstract
The depletion of disruptive variation caused by purifying natural selection (constraint) has been widely used to investigate protein-coding genes underlying human disorders 1-4, but attempts to assess constraint for non-protein-coding regions have proved more difficult. Here we aggregate, process and release a dataset of 76,156 human genomes from the Genome Aggregation Database (gnomAD)-the largest public open-access human genome allele frequency reference dataset-and use it to build a genomic constraint map for the whole genome (genomic non-coding constraint of haploinsufficient variation (Gnocchi)). We present a refined mutational model that incorporates local sequence context and regional genomic features to detect depletions of variation. As expected, the average constraint for protein-coding sequences is stronger than that for non-coding regions. Within the non-coding genome, constrained regions are enriched for known regulatory elements and variants that are implicated in complex human diseases and traits, facilitating the triangulation of biological annotation, disease association and natural selection to non-coding DNA analysis. More constrained regulatory elements tend to regulate more constrained protein-coding genes, which in turn suggests that non-coding constraint can aid the identification of constrained genes that are as yet unrecognized by current gene constraint metrics. We demonstrate that this genome-wide constraint map improves the identification and interpretation of functional human genetic variation.
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“Neutral, non-disease causing SALL1 variants (predicted loss-of-function, pLoF) were obtained from the gnomAD 48 database (v4.1.0, https://gnomad.broadinstitute.org/), with the following selection criteria: >2 cases found for each specific variant, no flag associated with dubious sequencing quality or possible pathogenicity.”
From Tetramerisation governs SALL transcription factor function in development and disease (2025) · cites this paper as [48]
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“we found that SALL1 is depleted of similar mutations in the healthy population, as a gnomAD 48 database (v4.1.0, https://gnomad.broadinstitute.org/) search identified only three variants, all at the C-terminus of the protein after SALL1 ZFC4”
From Tetramerisation governs SALL transcription factor function in development and disease (2025) · cites this paper as [48]
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“We note that there are many SNPs common (>5%) in these Polynesian sequences that are entirely absent from gnomAD (Fig. 1B) (6).”
From Message in a bottleneck: Nested founder effects from French Polynesia to Rapa Nui and Hawaiʻi (2026) · cites this paper as [6]
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“For inclusion on these population-specific screening panels, the ACMG recommends a carrier frequency of >1/200 (5, 6).”
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“38 A cutoff point of 42 is currently considered an US Food and Drug Administration-approved biomarker to select ovarian cancer patients for PARP inhibition, 39 which we used to differentiate between deficiency and proficiency in this study.”
Massively parallel quantification of mutational impact on IAPP amyloid formation
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“Comparing nucleation scores to allele frequency in the population and in diabetes patients 50 IAPP substitutions have been identi fi ed in the human population, but their clinical signi fi cance remains unknown 69 .”
Probing Electrostatics in a DNA Repair Enzyme with a pH-Sensitive Nitroxyl Spin Label
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“Population-stratified reference allele frequencies for the AFC defense layer are derived from the respective dataset panels or gnomAD v4 [34].”
Biallelic variants in FAT3 cause axonal neuropathy with multisystem neurodevelopmental features
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Comprehensive overview of the global pharmacogenetic and functional variability in NUDT15
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“In addition to published studies, we included population frequency data from the Genome Aggregation Database (gnomAD) [6], the Phase 3 1000 Genomes Project [2], the All of Us Research Program (2024) and the Norwegian Variant Frequency Database (https://variant.norgene.no/).”
Clinical features of syndromic microphthalmia in two novel RARB variants
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InfluentialComprehensive mutagenesis defines the functional landscape of human α-tubulin
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Xenbase: A Guide to the Xenopus Genetics and Genomics Knowledgebase
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Predicting genome-wide functional constraints with GPN-Star
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Population-scale immune multiome atlas reveals regulatory disease mechanisms
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Self-citationC and G are frequently mutated into T and A in coding regions of human genes
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Rare predicted deleterious FEZF2 variants are associated with a neurodevelopmental phenotype
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Self-citationIdentification and functional analysis of rare HECTD1 missense variants in human neural tube defects
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Destabilization and Degradation of a Disease-Linked PGM1 Protein Variant
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Investigating the Protective Role of the Mitochondrial 2158 T > C Variant in Parkinson's Disease
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Metadata
- Authors
- Chen, S., Francioli, L. C., Goodrich, J. K., Collins, R. L., Kanai, M., Wang, Q., Alföldi, J., Watts, N. A., Vittal, C., Gauthier, L. D., Poterba, T., Wilson, M. W., Tarasova, Y., Phu, W., Grant, R., Yohannes, M. T., Koenig, Z., Farjoun, Y., Banks, E., Donnelly, S., Gabriel, S., Gupta, N., Ferriera, S., Tolonen, C., Novod, S., Bergelson, L., Roazen, D., Ruano-Rubio, V., Covarrubias, M., Llanwarne, C., Petrillo, N., Wade, G., Jeandet, T., Munshi, R., Tibbetts, K., Genome Aggregation Database Consortium, Abreu, M., Aguilar Salinas, C. A., Ahmad, T., Albert, C. M., Ardissino, D., Armean, I. M., Atkinson, E. G., Atzmon, G., Barnard, J., Baxter, S. M., Beaugerie, L., Benjamin, E. J., Benjamin, D., Boehnke, M., Bonnycastle, L. L., Bottinger, E. P., Bowden, D. W., Bown, M. J., Brand, H., Brant, S., Brookings, T., Bryant, S., Calvo, S. E., Campos, H., Chambers, J. C., Chan, J. C., Chao, K. R., Chapman, S., Chasman, D. I., Chisholm, R., Cho, J., Chowdhury, R., Chung, M. K., Chung, W. K., Cibulskis, K., Cohen, B., Connolly, K. M., Correa, A., Cummings, B. B., Dabelea, D., Danesh, J., Darbar, D., Darnowsky, P., Denny, J., Duggirala, R., Dupuis, J., Ellinor, P. T., Elosua, R., Emery, J., England, E., Erdmann, J., Esko, T., Evangelista, E., Fatkin, D., Florez, J., Franke, A., Fu, J., Färkkilä, M., Garimella, K., Gentry, J., Getz, G., Glahn, D. C., Glaser, B., Glatt, S. J., Goldstein, D., Gonzalez, C., Groop, L., Gudmundsson, S., Haessly, A., Haiman, C., Hall, I., Hanis, C. L., Harms, M., Hiltunen, M., Holi, M. M., Hultman, C. M., Jalas, C., Kallela, M., Kaplan, D., Kaprio, J., Kathiresan, S., Kenny, E. E., Kim, B.-J., Kim, Y. J., King, D., Kirov, G., Kooner, J., Koskinen, S., Krumholz, H. M., Kugathasan, S., Kwak, S. H., Laakso, M., Lake, N., Langsford, T., Laricchia, K. M., Lehtimäki, T., Lek, M., Lipscomb, E., Loos, R. J. F., Lu, W., Lubitz, S. A., Luna, T. T., Ma, R. C. W., Marcus, G. M., Marrugat, J., Mattila, K. M., McCarroll, S., McCarthy, M. I., McCauley, J. L., McGovern, D., McPherson, R., Meigs, J. B., Melander, O., Metspalu, A., Meyers, D., Minikel, E. V., Mitchell, B. D., Mootha, V. K., Naheed, A., Nazarian, S., Nilsson, P. M., O’Donovan, M. C., Okada, Y., Ongur, D., Orozco, L., Owen, M. J., Palmer, C., Palmer, N. D., Palotie, A., Park, K. S., Pato, C., Pulver, A. E., Rader, D., Rahman, N., Reiner, A., Remes, A. M., Rhodes, D., Rich, S., Rioux, J. D., Ripatti, S., Roden, D. M., Rotter, J. I., Sahakian, N., Saleheen, D., Salomaa, V., Saltzman, A., Samani, N. J., Samocha, K. E., Sanchis-Juan, A., Scharf, J., Schleicher, M., Schunkert, H., Schönherr, S., Seaby, E. G., Shah, S. H., Shand, M., Sharpe, T., Shoemaker, M. B., Shyong, T., Silverman, E. K., Singer-Berk, M., Sklar, P., Smith, J. T., Smith, J. G., Soininen, H., Sokol, H., Son, R. G., Soto, J., Spector, T., Stevens, C., Stitziel, N. O., Sullivan, P. F., Suvisaari, J., Tai, E. S., Taylor, K. D., Teo, Y. Y., Tsuang, M., Tuomi, T., Turner, D., Tusie-Luna, T., Vartiainen, E., Vawter, M., Wang, L., Wang, A., Ware, J. S., Watkins, H., Weersma, R. K., Weisburd, B., Wessman, M., Whiffin, N., Wilson, J. G., Xavier, R. J., O’Donnell-Luria, A., Solomonson, M., Seed, C., Martin, A. R., Talkowski, M. E., Rehm, H. L., Daly, M. J., Tiao, G., Neale, B. M., MacArthur, D. G., & Karczewski, K. J.
- Affiliations
- Broad Institute (US)
- Lady Davis Institute for Medical Research (CA)
- University of Miami (US)
- Peninsula College of Medicine and Dentistry (GB)
- Brigham and Women's Hospital (US)
- University of Parma (IT)
- Albert Einstein College of Medicine (US)
- Cleveland Clinic (US)
- Sorbonne Université (FR)
- Boston University (US)
- University of Michigan (US)
- National Institutes of Health (US)
- Wake Forest University Health Sciences (US)
- University of Leicester (GB)
- Harvard University (US)
- Rutgers, The State University of New Jersey (US)
- Imperial College Healthcare NHS Trust (GB)
- Chinese University of Hong Kong (HK)
- Northwestern University (US)
- Icahn School of Medicine at Mount Sinai (US)
- University of Cambridge (GB)
- Columbia University Irving Medical Center (US)
- University of Mississippi Medical Center (US)
- Colorado School of Public Health (US)
- University of Illinois Chicago (US)
- Vanderbilt University Medical Center (US)
- Texas A&M University – San Antonio (US)
- University of Lübeck (DE)
- Victor Chang Cardiac Research Institute (AU)
- University of Helsinki (FI)
- Boston Children's Hospital (US)
- SUNY Upstate Medical University (US)
- University of Southern California (US)
- Washington University in St. Louis (US)
- The University of Texas Health Science Center at Houston (US)
- Columbia University (US)
- University of Eastern Finland (FI)
- Helsinki University Hospital (FI)
- Karolinska Institutet (SE)
- Korea National Institute of Health (KR)
- Cardiff University (GB)
- Finnish Institute for Health and Welfare (FI)
- Yale New Haven Hospital (US)
- Emory University (US)
- Seoul National University (KR)
- Yale University (US)
- Tampere University (FI)
- University of Copenhagen (DK)
- Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán (MX)
- University of California, San Francisco (US)
- Centro de Investigación en Red en Enfermedades Cardiovasculares (ES)
- Centre for Human Genetics (GB)
- Cedars-Sinai Medical Center (US)
- Ottawa Heart Institute (CA)
- Lund University (SE)
- University of Tartu (EE)
- University of Arizona (US)
- University of Maryland, Baltimore (US)
- International Centre for Diarrhoeal Disease Research (BD)
- Johns Hopkins University (US)
- Institute for Open and Transdisciplinary Research Initiatives (JP)
- National Institute of Genomic Medicine (MX)
- University of Dundee (GB)
- Children's Hospital of Philadelphia (US)
- Institute of Cancer Research (GB)
- University of Washington (US)
- Oulu University Hospital (FI)
- University of Virginia (US)
- Montreal Heart Institute (CA)
- The Lundquist Institute (US)
- Center for Non-Communicable Diseases (PK)
- Deutsches Herzzentrum München (DE)
- Innsbruck Medical University (AT)
- Duke University (US)
- Vanderbilt University (US)
- National University of Singapore (SG)
- Inserm (FR)
- King's College London (GB)
- University of North Carolina at Chapel Hill (US)
- University of California San Diego (US)
- Hebrew University of Jerusalem (IL)
- University of California, Irvine (US)
- University of Oxford (GB)
- University Medical Center Groningen (NL)
- Beth Israel Deaconess Medical Center (US)
- Corresponding author
- Chen, Siwei
- Karczewski, Konrad J.
- ORCID
- Chen, Siwei
- Francioli, Laurent C.
- Goodrich, Julia K.
- Collins, Ryan L.
- Kanai, Masahiro
- Wang, Qingbo
- Alföldi, Jessica
- Poterba, Timothy
- Wilson, Michael W.
- Phu, William
- Farjoun, Yossi
- Banks, Eric
- Donnelly, Stacey
- Gabriel, Stacey
- Gupta, Namrata
- Abreu, Maria
- Ahmad, Tariq
- Albert, Christine M.
- Ardissino, Diego
- Armean, Irina M.
- Atkinson, Elizabeth G.
- Atzmon, Gil
- Barnard, John
- Baxter, Samantha M.
- Beaugerie, Laurent
- Benjamin, Emelia J.
- Boehnke, Michael
- Bonnycastle, Lori L.
- Bowden, Donald W.
- Bown, Matthew J.
- Brand, Harrison
- Brant, Steven
- Calvo, Sarah E.
- Campos, Hannia
- Chambers, John C.
- Chan, Juliana C.
- Chao, Katherine R.
- Chapman, Sinéad
- Chasman, Daniel I.
- Chisholm, Rex
- Cho, Judy
- Chowdhury, Rajiv
- Chung, Mina K.
- Chung, Wendy K.
- Cibulskis, Kristian
- Cohen, Bruce
- Correa, Adolfo
- Cummings, Beryl B.
- Dabelea, Dana
- Danesh, John
- Darbar, Dawood
- Denny, Joshua
- Duggirala, Ravindranath
- Dupuis, Josée
- Ellinor, Patrick T.
- Erdmann, Jeanette
- Esko, Tõnu
- Evangelista, Emily
- Fatkin, Diane
- Fu, Jack
- Färkkilä, Martti
- Garimella, Kiran
- Getz, Gad
- Glahn, David C.
- Glatt, Stephen J.
- Goldstein, David
- Groop, Leif
- Gudmundsson, Sanna
- Haessly, Andrea
- Haiman, Christopher
- Hall, Ira
- Hanis, Craig L.
- Harms, Matthew
- Hiltunen, Mikko
- Holi, Matti M.
- Hultman, Christina M.
- Jalas, Chaim
- Kallela, Mikko
- Kaprio, Jaakko
- Kathiresan, Sekar
- Kenny, Eimear E.
- Kim, Bong-Jo
- Kim, Young Jin
- Kirov, George
- Kooner, Jaspal
- Koskinen, Seppo
- Krumholz, Harlan M.
- Kugathasan, Subra
- Kwak, Soo Heon
- Laakso, Markku
- Lake, Nicole
- Laricchia, Kristen M.
- Lehtimäki, Terho
- Lek, Monkol
- Loos, Ruth J. F.
- Lu, Wenhan
- Lubitz, Steven A.
- Marcus, Gregory M.
- Marrugat, Jaume
- McCarroll, Steven
- McCarthy, Mark I.
- McCauley, Jacob L.
- McGovern, Dermot
- McPherson, Ruth
- Meigs, James B.
- Melander, Olle
- Metspalu, Andres
- Meyers, Deborah
- Minikel, Eric V.
- Mitchell, Braxton D.
- Mootha, Vamsi K.
- Naheed, Aliya
- Nazarian, Saman
- Nilsson, Peter M.
- O’Donovan, Michael C.
- Okada, Yukinori
- Orozco, Lorena
- Owen, Michael J.
- Palotie, Aarno
- Park, Kyong Soo
- Pato, Carlos
- Pulver, Ann E.
- Rahman, Nazneen
- Reiner, Alex
- Rich, Stephen
- Rioux, John D.
- Ripatti, Samuli
- Roden, Dan M.
- Rotter, Jerome I.
- Saleheen, Danish
- Salomaa, Veikko
- Saltzman, Andrea
- Samani, Nilesh J.
- Samocha, Kaitlin E.
- Scharf, Jeremiah
- Schunkert, Heribert
- Schönherr, Sebastian
- Seaby, Eleanor G.
- Shah, Svati H.
- Shand, Megan
- Shoemaker, Moore B.
- Silverman, Edwin K.
- Sklar, Pamela
- Smith, Jonathan T.
- Soininen, Hilkka
- Sokol, Harry
- Son, Rachel G.
- Spector, Tim
- Stevens, Christine
- Stitziel, Nathan O.
- Sullivan, Patrick F.
- Suvisaari, Jaana
- Tai, E. Shyong
- Taylor, Kent D.
- Tsuang, Ming
- Turner, Dan
- Vartiainen, Erkki
- Vawter, Marquis
- Wang, Lily
- Ware, James S.
- Watkins, Hugh
- Weersma, Rinse K.
- Weisburd, Ben
- Whiffin, Nicola
- Wilson, James G.
- Xavier, Ramnik J.
- O’Donnell-Luria, Anne
- Solomonson, Matthew
- Martin, Alicia R.
- Talkowski, Michael E.
- Rehm, Heidi L.
- Daly, Mark J.
- Tiao, Grace
- Neale, Benjamin M.
- MacArthur, Daniel G.
- Karczewski, Konrad J.
- Venue
- Nature
- Published
- 2023-12-06
- Volume
- 625
- Issue
- 7993
- Pages
- 92-100
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC11629659
- OpenAlex
- W4389367121
- Cited by
- 1,727
- References
- 90
- Citations by year
- 2026: 520 · 2025: 642 · 2024: 442 · 2023: 121
- FWCI
- 286.54
- Type
- journal article
- Language
- en
- Update notices
- correction (2024-01-15)
- Open access
- green
- doi.org
- Licence
- Locations
- Nature (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- PubMed (publishedVersion)
- Research at the University of Copenhagen (University of Copenhagen) (publishedVersion, other-oa)
- University of Groningen research database (University of Groningen / Centre for Information Technology) (publishedVersion)
- PubMed Central (acceptedVersion, other-oa)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Discovery Research Portal (University of Dundee) (submittedVersion)
- Lund University Publications (Lund University) (submittedVersion)
- STM:n Hallinnonalan avoin julkaisuarkisto (Julkari) (submittedVersion)
- Funders
- Wellcome Trust (107469/Z/15/Z)
- National Institutes of Health
- Medical Research Council (MR/L010305/1)
- National Institute of Mental Health (R01MH115957)
- National Human Genome Research Institute (U24HG011450)
- National Institute of Diabetes and Digestive and Kidney Diseases (U54DK105566)
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (R01HD081256)
- 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 › Evolution and Genetic Dynamics
- Keywords
- purifying selection, non-coding DNA, regulatory elements, gnocchi, allele frequency, complex diseases, genetic variants, protein-coding genes, sequence context
- MeSH terms
- Chromosome Mapping, Gene Frequency, Humans, Models, Genetic, Mutation, Selection, Genetic, Genetic Variation, Genome, Human, Access to Information, Genomics, Databases, Genetic, Datasets as Topic
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.
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