Most genetic risk for autism resides with common variation
Open accessAbstract
A key component of genetic architecture is the allelic spectrum influencing trait variability. For autism spectrum disorder (herein termed autism), the nature of the allelic spectrum is uncertain. Individual risk-associated genes have been identified from rare variation, especially de novo mutations. From this evidence, one might conclude that rare variation dominates the allelic spectrum in autism, yet recent studies show that common variation, individually of small effect, has substantial impact en masse. At issue is how much of an impact relative to rare variation this common variation has. Using a unique epidemiological sample from Sweden, new methods that distinguish total narrow-sense heritability from that due to common variation and synthesis of results from other studies, we reach several conclusions about autism's genetic architecture: its narrow-sense heritability is ∼52.4%, with most due to common variation, and rare de novo mutations contribute substantially to individual liability, yet their contribution to variance in liability, 2.6%, is modest compared to that for heritable variation.
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Considering the overall population, the contribution of de novo mutations to ASD risk is quite small (~3%).
“Considering the overall population, the contribution of de novo mutations to ASD risk is quite small (~3%) 32 .”
From Autism spectrum disorder (2020) · cites this paper as [32]
The Abstract reports that de novo CNV and loss-of-function mutations explain 2.6% of the variance in liability to autism, consistent with the claim’s approximate 3% figure. But it specifies that this estimate comes from a sample enriched for those mutations, not the overall population, and measures variance in liability rather than the contribution to risk for an individual. (LLM, conf=0.87)
Experimental — accuracy not yet measuredTwin and family studies consistently demonstrate that ASD has a particularly large genetic contribution, with estimated heritability ranging from ~40 to 90%.
“Twin and family studies consistently demonstrate that ASD has a particularly large genetic contribution, with estimated heritability ranging from ~40 to 90% 31,32 .”
From Autism spectrum disorder (2020) · cites this paper as [32]
The paper’s heritability discussion (section labeled Abstract; page unavailable) reports a Swedish family-study estimate of 54% and a recent twin-study estimate of 38%, supporting a substantial genetic contribution. But it places early twin estimates close to 100%, above the stated ~90% upper bound, and cautions that those estimates rely on dubious assumptions. The studies therefore do not support the claim’s unqualified consistency or its precise range. (LLM, conf=0.84)
Experimental — accuracy not yet measuredASD affects 1-1.5% of individuals and is highly heritable, with both common and rare variants contributing to its etiology.
“ASD affects 1-1.5% of individuals and is highly heritable, with both common and rare variants contributing to its etiology 1-4 .”
From Identification of common genetic risk variants for autism spectrum disorder (2019) · cites this paper as [2]
The Abstract reports heritability of approximately 54% and contributions from both common and rare variants. Online Methods (Ascertainment of subjects; page unavailable) reports approximately 100 cases per 10,000—about 1%—for broad autism in the Swedish sample. It does not establish the full 1–1.5% range for individuals generally. (LLM, conf=0.83)
Experimental — accuracy not yet measuredCommon variation plays an important role in ASD risk, and recent GWASs reveal a handful of ASD-associated loci.
“Common variation plays an important role in ASD risk (Gaugler et al., 2014), and recent genome-wide association studies (GWASs) reveal a handful of ASD-associated loci (Grove et al., 2019)”
From Large-Scale Exome Sequencing Study Implicates Both Developmental and Functional Changes in the Neurobiology of Autism (2020) · cites this paper as Gaugler et al., 2014
De novo mutations, mostly copy number variants and gene disrupting point mutations, have larger individual effects but collectively explain less than 5% of the overall liability and far less of the heritability.
“By contrast, de novo mutations, mostly copy number variants (CNVs) and gene disrupting point mutations, have larger individual effects, but collectively explain <5% of the overall liability 1-3 and far less of the heritability.”
From Identification of common genetic risk variants for autism spectrum disorder (2019) · cites this paper as [2]
Common genetic variants have been estimated to account for a major part of ASD liability.
“Common variants have been estimated to account for a major part of ASD liability 2 as has been observed for other common neuropsychiatric disorders.”
From Identification of common genetic risk variants for autism spectrum disorder (2019) · cites this paper as [2]
The SNP heritability for autism is higher than estimates from iPSYCH but lower than estimates from AGRE and PAGES cohorts.
“which is higher than estimates from iPSYCH16 but lower than estimates from the AGRE55 and PAGES56 cohorts.”
From Genetic correlates of phenotypic heterogeneity in autism (2022) · cites this paper as [56]
Male-female differences are less clear in the context of ASD's common, inherited genetic influences, which constitute the majority of genetic risk for ASD.
“Male-female differences are less clear in the context of ASD’s common, inherited genetic influences, which constitute the majority of genetic risk for ASD.14”
From The female protective effect against autism spectrum disorder (2022) · cites this paper as [14]
ASD is associated with a large number of genetic mutations, including possibly hundreds of rare causal variants and over one hundred common variants of small effect.
“Instead, ASD seems to be associated with a large number of genetic mutations, including possibly hundreds of rare causal variants and over one hundred common variants of small effect18,19.”
From Immune mediators in the brain and peripheral tissues in autism spectrum disorder (2015) · cites this paper as [18]
Common variation dominates heritable risk for schizophrenia and autism spectrum disorder.
“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 Gaugler et al., 2014
When directly examined, polygenic risk combines additively with major mutation burden.
“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 Gaugler et al., 2014
Estimates of ASD heritability explained by common SNPs range from 17% to 52%.
“Estimates of the heritability of ASD explained by common SNPs range from 17% (Autism Spectrum Disorders Working Group of The Psychiatric Genomics, 2017; Cross-Disorder Group of the Psychiatric Genomics et al., 2013) to 52% (Gaugler et al., 2014).”
From Getting to the cores of autism (2019) · cites this paper as Gaugler et al., 2014
The genetic contributions to ASD are highly heterogeneous but may converge on common pathways that are not yet well understood.
“These contributions are profoundly heterogeneous but may converge on common pathways that are not yet well understood1–3.”
From Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism (2016) · cites this paper as [1]
Autism spectrum disorder has a substantial genetic component.
“Autism spectrum disorder (ASD) involves substantial genetic contributions.”
From Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism (2016) · cites this paper as [1]
Common SNP variation contributes to ASD risk in carriers of either a de novo CNV or a de novo loss-of-function SNV.
“but common variation, in the form of SNPs, contributes in either case.”
From Genetics and genomics of autism spectrum disorder: embracing complexity (2015) · cites this paper as [11]
The findings support a model in which inherited common and rare variation create a susceptibility substrate, and additional high-risk genetic and/or non-genetic factors push liability past a threshold to cause ASD.
“These findings are consistent with a model whereby inherited variation, both common (11) and rare (26,28), defines a substrate of susceptibility, and additional high-risk genetic (including de novo, recessive and X-linked variation) and/or non-genetic factors then act on this substrate to surpass the liability threshold that results in ASD (Fig. 1).”
From Genetics and genomics of autism spectrum disorder: embracing complexity (2015) · cites this paper as [11]
Polygenic risk from many SNPs is a major determinant of ASD variance.
“However, polygenic risk due to a large number of SNPs is a major determinant of the variance for ASD (11,12,16) (Fig. 1).”
From Genetics and genomics of autism spectrum disorder: embracing complexity (2015) · cites this paper as [11]
About 80% of individuals with a de novo CNV and an ASD diagnosis would not be affected if they did not have the CNV.
“They found that ∼80% of the individuals with a de novo CNV and an ASD diagnosis would not be affected if they did not have the CNV”
From Genetics and genomics of autism spectrum disorder: embracing complexity (2015) · cites this paper as [11]
Gaugler et al. estimated the probability that carriers of de novo CNVs or SNVs would be affected if they had not carried those mutations, using a well-defined ASD cohort.
“Gaugler et al. (11) provide a clear example by estimating the probability for carriers of de novo mutations (CNV or SNV) to be affected if they were not carriers of these mutations, using a well defined ASD cohort (11).”
From Genetics and genomics of autism spectrum disorder: embracing complexity (2015) · cites this paper as [11]
About 57% of individuals with a de novo loss-of-function SNV and an ASD diagnosis would not be affected if they did not have the SNV.
“and 57% of the individuals with a de novo loss-of-function SNV and an ASD diagnosis would not be affected if they did not have the SNV”
From Genetics and genomics of autism spectrum disorder: embracing complexity (2015) · cites this paper as [11]
Non-genetic etiologies may account for 30-41% of the risk for ASD, and such factors may act independently or in combination with genetic factors.
“Non-genetic etiologies may account for 30–41% of the risk for ASD [113], and such factors may act independently or in combination with genetic factors [113].”
From The ASD Living Biology: from cell proliferation to clinical phenotype (2019) · cites this paper as [113]
Next-generation sequencing and genome-wide association studies generally find a complex and varied genomic landscape in autism.
“researchers have utilized the advanced techniques of next-generation sequencing and genome-wide association studies (GWAS) in an attempt to divine the genetic causes of autism, generally finding a complex and varied genomic landscape (Abrahams and Geschwind, 2008;Gaugler et al, 2014;Michel et al, 2012).”
From The Role of the Immune System in Autism Spectrum Disorder (2017) · cites this paper as Gaugler et al, 2014
Common variants may significantly contribute to a large proportion (up to 60%) of genetic liability for ASD.
“common variants may also significantly contribute to a large proportion (up to 60%) of genetic liability for ASD,7, 8”
From Maternal immune activation dysregulation of the fetal brain transcriptome and relevance to the pathophysiology of autism spectrum disorder (2018) · cites this paper as [8]
ASD is one of the most heritable psychiatric disorders, with heritability estimated at about 50% and monozygotic twin concordance rates between 70 and 90%.
“Twin, family and population-based studies have shown ASD to be one of the most heritable of all psychiatric disorders, with heritability estimated at ~50% (see reviews in [119, 310]) and monozygotic twin concordance rates between 70 to 90% [1, 113, 139, 304, 344].”
From Autism spectrum disorder: neuropathology and animal models (2017) · cites this paper as [119]
Common genetic variation explains roughly half of the genetic risk in ASD.
“Importantly, common genetic variation explains roughly half of this genetic risk in ASD [7], making the genome-wide association study (GWAS) an efficient design for identifying risk variants.”
The same genetic risk factors can underlie many diagnoses, from autism spectrum disorder to schizophrenia.
“Furthermore, a common source may drive such comorbidity; for example, the same genetic risk factors can underlie many diagnoses (4,15,16)—from autism spectrum disorder (ASD) to schizo- phrenia.”
From Methods and challenges for assessing heterogeneity (2020) · cites this paper as [16]
Reported differences in genetic population structure between Finland and the rest of Europe could partly account for the higher shared environment and lower heritability estimates for ASD in Finland.
“Indeed, studies have suggested differences in genetic population structure between Finland and the rest of Europe, 29,30 which could partially explain the increased shared environment and decreased heritability estimates for ASD in Finland.”
From Association of Genetic and Environmental Factors With Autism in a 5-Country Cohort (2019) · cites this paper as [30]
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- Authors
- Gaugler, T., Klei, L., Sanders, S. J., Bodea, C. A., Goldberg, A. P., Lee, A. B., Mahajan, M., Manaa, D., Pawitan, Y., Reichert, J., Ripke, S., Sandin, S., Sklar, P., Svantesson, O., Reichenberg, A., Hultman, C. M., Devlin, B., Roeder, K., & Buxbaum, J. D.
- Affiliations
- Carnegie Mellon University (US)
- University of Pittsburgh (US)
- University of California, San Francisco (US)
- Icahn School of Medicine at Mount Sinai (US)
- Massachusetts General Hospital (US)
- Karolinska Institutet (SE)
- Corresponding author
- Roeder, Kathryn
- Buxbaum, Joseph D
- ORCID
- Venue
- Nature Genetics
- Published
- 2014-07-20
- Volume
- 46
- Issue
- 8
- Pages
- 881-885
- ISSN
- 1061-4036 (ISSN-L)
- 1546-1718
- PMC
- PMC4137411
- OpenAlex
- W2033021653
- Semantic Scholar
- ed99d8ed8d1f83ac18443f3b73fbc0b9038250be
- Cited by
- 1,239
- References
- 36
- Citations by year
- 2026: 60 · 2025: 82 · 2024: 87 · 2023: 82 · 2022: 108 · 2021: 131 · 2020: 148 · 2019: 115 · 2018: 97 · 2017: 115 · 2016: 106 · 2015: 86 · 2014: 22
- FWCI
- 61.18
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Genetics (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- Canadian Institutes of Health Research
- National Institute of Mental Health (MH-066673, MH 57881, R01MH061009, MH66766, R01MH077139, MH097849, R01MH097849, R01MH052708, MH095034, U54MH066673, MH06359, R01MH080647, R37MH057881, U10MH066766, MH 55284, MH081754, R01MH057881, R01MH081754, MH52708, MH080647, R56MH097849, MH057881, R01MH095034, MH077139, MH061009)
- National Institute of Neurological Disorders and Stroke (NS026630, NS049261, P01NS026630, R01NS049261, R01NS042165, NS-042165)
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (P50HD055751, P50HD055782, HD055784, HD055751, P50HD055784, HD055782, HD35465)
- Topics
- Life Sciences › Neuroscience › Cognitive Neuroscience › Autism Spectrum Disorder Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetics and Neurodevelopmental Disorders
- Keywords
- autism spectrum disorder, genetic architecture, common genetic variants, rare variants, de novo mutations, narrow-sense heritability
- MeSH terms
- Adolescent, Adult, Aged, Alleles, Autistic Disorder, Child, Humans, Middle Aged, Mutation, Risk Factors, Sweden, Genetic Predisposition to Disease, Polymorphism, Single Nucleotide, Young Adult
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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