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A polygenic burden of rare disruptive mutations in schizophrenia
Open accessAbstract
Schizophrenia is a common disease with a complex aetiology, probably involving multiple and heterogeneous genetic factors. Here, by analysing the exome sequences of 2,536 schizophrenia cases and 2,543 controls, we demonstrate a polygenic burden primarily arising from rare (less than 1 in 10,000), disruptive mutations distributed across many genes. Particularly enriched gene sets include the voltage-gated calcium ion channel and the signalling complex formed by the activity-regulated cytoskeleton-associated scaffold protein (ARC) of the postsynaptic density, sets previously implicated by genome-wide association and copy-number variation studies. Similar to reports in autism, targets of the fragile X mental retardation protein (FMRP, product of FMR1) are enriched for case mutations. No individual gene-based test achieves significance after correction for multiple testing and we do not detect any alleles of moderately low frequency (approximately 0.5 to 1 per cent) and moderately large effect. Taken together, these data suggest that population-based exome sequencing can discover risk alleles and complements established gene-mapping paradigms in neuropsychiatric disease.
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“These findings support our model in which CYFIP1 regulation of calcium channel subunits compromise intracellular calcium levels, resulting in delayed axonal development10,84,85 (Fig. 7).”
From CYFIP1 governs the development of cortical axons by modulating calcium availability (2025) · cites this paper as [10]
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“Additionally, a polygenic pattern including a rare heterozygous disruptive nonsense variant, p.Arg624Ter, in CYFIP1 was detected in a patient diagnosed with SCZ115 (Table 2n).”
From The WAVE complex in developmental and adulthood brain disorders (2025) · cites this paper as [115]
Experimental — accuracy not yet measuredIn the citing paper
“direct comparisons of the contributions of common and rare genetic variation show that common variation dominates heritable risk for SCZ and ASD (Gaugler et al., 2014; Purcell et al., 2014)”
From Defining the genetic, genomic, cellular, and diagnostic architectures of psychiatric disorders (2019) · cites this paper as Purcell et al., 2014
In the citing paper
“In the instances where this has been studied directly, polygenic risk acts additively with major mutational burdens (Gaugler et al., 2014; Niemi et al., 2018; Purcell et al., 2014; Weiner et al., 2017).”
From Defining the genetic, genomic, cellular, and diagnostic architectures of psychiatric disorders (2019) · cites this paper as Purcell et al., 2014
In the citing paper
“Thus, many severe mutations do not converge on one specific phenotype but instead seem to cause a range of clinical disorders74,76,80,81,84,87,91.”
From Systems biology and gene networks in neurodevelopmental and neurodegenerative disorders (2015) · cites this paper as [81]
In the citing paper
“Additionally, whole-exome sequencing studies of other neurodevelopmental disorders have found enrichment for FMRP targets in rare mutations in schizophrenia81, intellectual disability68 and epilepsy78.”
From Systems biology and gene networks in neurodevelopmental and neurodegenerative disorders (2015) · cites this paper as [81]
In the citing paper
“Earlier schizophrenia sequencing studies have established that ultra-rare and de novo mutations contribute to risk as a category, and have prioritized disease-relevant tissues and processes, specifically observing an enrichment in neuronal genes and synaptic processes9,11,19–23.”
From Rare coding variants in ten genes confer substantial risk for schizophrenia (2022) · cites this paper as [19]
In the citing paper
“among 5,092 (of the 12,332) individuals who were also part of an earlier sequencing study9, the additional data allowed us to re-classify ~66% of variants that had been “singletons” as segregating variants (not URVs in the current analysis).”
From Increased burden of ultra-rare protein-altering variants among 4,877 individuals with schizophrenia (2016) · cites this paper as [9]
In the citing paper
“A strong and consistent finding in exome-sequencing studies of schizophrenia involves an excess of variants in genes whose mRNAs are bound by the fragile X mental retardation protein (FMRP)9,12,27.”
From Increased burden of ultra-rare protein-altering variants among 4,877 individuals with schizophrenia (2016) · cites this paper as [9]
In the citing paper
“The observed enrichment was consistent across data from previously analyzed exomes9 and newly generated data (Supplementary Fig. 5); as the previously analyzed exomes were sequenced across randomized batches with equal number of cases and controls in each batch, this provides additional evidence that the enrichment is not due to technical effects.”
From Increased burden of ultra-rare protein-altering variants among 4,877 individuals with schizophrenia (2016) · cites this paper as [9]
In the citing paper
“The fact that an analysis of the current scale (4,877 cases, 6,203 controls, and 45,376 other genomes used to help identify ultra-rare variants) did not implicate individual genes of large effect in an unbiased exome-wide search – while documenting a very clear exome-wide elevation of hundreds of pathogenic variants across 4,877 individuals affected with schizophrenia relative to controls – lends”
From Increased burden of ultra-rare protein-altering variants among 4,877 individuals with schizophrenia (2016) · cites this paper as [9]
In the citing paper
“Psychiatric cases with a diagnosis of schizophrenia or bipolar disorder were ascertained from the Swedish National Hospital Discharge Register as described in previous studies9,50, which captures all inpatient hospitalizations. Controls were randomly selected from population registers.”
From Increased burden of ultra-rare protein-altering variants among 4,877 individuals with schizophrenia (2016) · cites this paper as [9]
In the citing paper
“SCZ is truly complex and appears to result from a myriad of genetic variants exerting small effects on disease risk4,5, conforming closely to a classical polygenic model.”
From Gene expression elucidates functional impact of polygenic risk for schizophrenia (2016) · cites this paper as [5]
In the citing paper
“SCZ is truly complex and appears to result from a myriad of genetic variants exerting small effects on disease risk4,5, conforming closely to a classical polygenic model.”
From Gene expression elucidates functional impact of polygenic risk for schizophrenia (2016) · cites this paper as [5]
In the citing paper
“The available data are incomplete but implicate synaptic components, including calcium channel subunits and post-synaptic elements5–7.”
From Gene expression elucidates functional impact of polygenic risk for schizophrenia (2016) · cites this paper as [5]
In the citing paper
“We note that strong, independent support of our findings comes from the observation that analyses of rare variants have also implicated postsynaptic pathways in SCZ etiology23,24, suggesting that both rare and common variants are relevant.”
From Psychiatric genome-wide association study analyses implicate neuronal, immune and histone pathways (2015) · cites this paper as [24]
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Metadata
- Authors
- Purcell, S. M., Moran, J. L., Fromer, M., Ruderfer, D., Solovieff, N., Roussos, P., O’Dushlaine, C., Chambert, K., Bergen, S. E., Kähler, A., Duncan, L., Stahl, E., Genovese, G., Fernández, E., Collins, M. O., Komiyama, N. H., Choudhary, J. S., Magnusson, P. K. E., Banks, E., Shakir, K., Garimella, K., Fennell, T., DePristo, M., Grant, S. G. N., Haggarty, S. J., Gabriel, S., Scolnick, E. M., Lander, E. S., Hultman, C. M., Sullivan, P. F., McCarroll, S. A., & Sklar, P.
- Affiliations
- Broad Institute (US)
- Icahn School of Medicine at Mount Sinai (US)
- Massachusetts General Hospital (US)
- Karolinska Institutet (SE)
- KU Leuven (BE)
- Wellcome Sanger Institute (GB)
- University of Edinburgh (GB)
- University of North Carolina at Chapel Hill (US)
- Corresponding author
- Purcell, Shaun M.
- ORCID
- Purcell, Shaun M.
- Moran, Jennifer L.
- Fromer, Menachem
- Ruderfer, Douglas
- Solovieff, Nadia
- Roussos, Panos
- Bergen, Sarah E.
- Kähler, Anna
- Duncan, Laramie
- Genovese, Giulio
- Fernández, Esperanza
- Collins, Mark O.
- Komiyama, Noboru H.
- Choudhary, Jyoti S.
- Magnusson, Patrik K. E.
- Banks, Eric
- Garimella, Kiran
- Fennell, Tim
- Grant, Seth G. N.
- Haggarty, Stephen J.
- Gabriel, Stacey
- Scolnick, Edward M.
- Lander, Eric S.
- Sullivan, Patrick F.
- McCarroll, Steven A.
- Sklar, Pamela
- Venue
- Nature
- Published
- 2014-01-22
- Volume
- 506
- Issue
- 7487
- Pages
- 185-190
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC4136494
- OpenAlex
- W2132297623
- Cited by
- 1,385
- References
- 52
- Citations by year
- 2026: 23 · 2025: 39 · 2024: 34 · 2023: 60 · 2022: 96 · 2021: 98 · 2020: 123 · 2019: 145 · 2018: 158 · 2017: 169 · 2016: 169 · 2015: 158 · 2014: 113
- FWCI
- 154.88
- Type
- journal article
- Language
- en
- Open access
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- White Rose Research Online (University of Leeds, The University of Sheffield, University of York) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Carolina Digital Repository (University of North Carolina at Chapel Hill) (submittedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- UNC Libraries
- Funders
- U.S. Department of Veterans Affairs (I01BX002395)
- Wellcome Trust
- European Commission (242167, 241995)
- Nederlandse Organisatie voor Wetenschappelijk Onderzoek (645-000-003)
- Karolinska Institutet
- Vetenskapsrådet (R01 MH077139)
- National Institutes of Health (241995)
- Stanley Center for Psychiatric Research, Broad Institute
- Medical Research Council
- National Heart, Lung, and Blood Institute
- National Institute of Mental Health (R01MH077139, T32MH017119, TT32MH017119, R01MH095088, RC2MH089905, R01MH095034, MH077139, R01MH091115, R01MH099126)
- National Human Genome Research Institute (U54HG003067, R01HG005827)
- Topics
- Health Sciences › Medicine › Psychiatry and Mental health › Schizophrenia research and treatment
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Keywords
- schizophrenia, polygenic burden, exome sequencing, activity-regulated cytoskeleton-associated protein, postsynaptic density, FMRP, glutamatergic synapses, autism spectrum disorder
- MeSH terms
- Disks Large Homolog 4 Protein, Autistic Disorder, Cytoskeletal Proteins, Female, Humans, Male, Membrane Proteins, Intellectual Disability, Mutation, Nerve Tissue Proteins, Schizophrenia, Calcium Channels, Receptors, N-Methyl-D-Aspartate, Multifactorial Inheritance, Intracellular Signaling Peptides and Proteins, Fragile X Messenger Ribonucleoprotein 1, Genome-Wide Association Study, DNA Copy Number Variations
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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