Autism genome-wide copy number variation reveals ubiquitin and neuronal genes
Open accessAbstract
Autism spectrum disorders (ASDs) are childhood neurodevelopmental disorders with complex genetic origins. Previous studies focusing on candidate genes or genomic regions have identified several copy number variations (CNVs) that are associated with an increased risk of ASDs. Here we present the results from a whole-genome CNV study on a cohort of 859 ASD cases and 1,409 healthy children of European ancestry who were genotyped with approximately 550,000 single nucleotide polymorphism markers, in an attempt to comprehensively identify CNVs conferring susceptibility to ASDs. Positive findings were evaluated in an independent cohort of 1,336 ASD cases and 1,110 controls of European ancestry. Besides previously reported ASD candidate genes, such as NRXN1 (ref. 10) and CNTN4 (refs 11, 12), several new susceptibility genes encoding neuronal cell-adhesion molecules, including NLGN1 and ASTN2, were enriched with CNVs in ASD cases compared to controls (P = 9.5 x 10(-3)). Furthermore, CNVs within or surrounding genes involved in the ubiquitin pathways, including UBE3A, PARK2, RFWD2 and FBXO40, were affected by CNVs not observed in controls (P = 3.3 x 10(-3)). We also identified duplications 55 kilobases upstream of complementary DNA AK123120 (P = 3.6 x 10(-6)). Although these variants may be individually rare, they target genes involved in neuronal cell-adhesion or ubiquitin degradation, indicating that these two important gene networks expressed within the central nervous system may contribute to the genetic susceptibility of ASD.
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Module 2 is rather homogeneous in terms of protein function, whereas M1 comprises diverse functional categories, including genes involved in the ubiquitin pathway and in cancer.
“Whereas module 2 is rather homogeneous in terms of protein function, M1 comprises diverse functional categories, including genes involved in the ubiquitin pathway and in cancer (see below), in line with previous observations57, 58.”
From Distinct selective forces and Neanderthal introgression shaped genetic diversity at genes involved in neurodevelopmental disorders (2017) · cites this paper as [57]
The paper’s Abstract identifies ubiquitin-pathway genes among its autism-associated CNV findings, supporting that part of the cited comparison. It does not describe M1 or M2 or establish the claim about cancer-related genes; those module descriptions are the citing authors’ own analysis. No page number is available in our copy. (LLM, conf=0.83)
Experimental — accuracy not yet measuredThe neurexin-1 (nrxn1) gene has been linked directly to ASD and SCZ.
“Of these, the neurexin-1 (nrxn1) gene has been linked directly to ASD and SCZ (Kim et al. 2008; Rujescu et al. 2009, Glessner et al. 2009; Ching et al. 2010; Gauthier et al. 2011).”
From Neurexin1α knockout in rats causes aberrant social behaviour: relevance for autism and schizophrenia (2025) · cites this paper as Glessner et al. 2009
The paper reports in its main text (indexed under Abstract; page unavailable) that NRXN1 deletions replicate an association with ASD in its cohorts. It does not link NRXN1 to schizophrenia; the schizophrenia association mentioned there concerns ASTN2 deletions. (LLM, conf=0.88)
Experimental — accuracy not yet measuredGenes previously implicated in ASD by rare variant findings have pointed to functional themes in ASD pathophysiology.
“Genes previously implicated in ASD by rare variant findings have pointed to functional themes in ASD pathophysiology 6,28 .”
From Functional impact of global rare copy number variation in autism spectrum disorders (2010) · cites this paper as [28]
Deletions and/or duplications at specific loci including 1q21.1, 15q11.2-13.1, 15q13.2-13.3, 16p11.2, 17q12, and 22q11.2 show evidence for association with ASD.
“These include deletions and/or duplications at specific loci, including: 1q21.1, 15q11.2-13.1, 15q13.2-13.3, 16p11.2, 17q12, and 22q11.2”
From Multiple recurrent de novo CNVs, including duplications of the 7q11.23 Williams syndrome region, are strongly associated with autism (2011) · cites this paper as Glessner et al., 2009
Recurrent structural variations involving NRXN1, CNTN4, NLGN1, ASTN2, PTCHD1, and DDX53 show evidence for association with ASD.
“recurrent structural variations involving one or a small number of genes, including: Neurexin 1 (NRXN1), Contactin 4 (CNTN4), Neuroligin 1 (NLGN1), Astrotactin 2 (ASTN2), and the contiguous genes Patched Domain Containing 1 (PTCHD1) and DEAD box Protein 53 (DDX53)”
From Multiple recurrent de novo CNVs, including duplications of the 7q11.23 Williams syndrome region, are strongly associated with autism (2011) · cites this paper as Glessner et al., 2009
For USP7, these processes, especially the ubiquitin pathway, have been linked to ASD pathogenesis before.
“for the latter, these biological processes, and the ubiquitin pathway in particular, have been previously implicated in ASD pathogenesis (Glessner et al., 2009)”
From Multiple recurrent de novo CNVs, including duplications of the 7q11.23 Williams syndrome region, are strongly associated with autism (2011) · cites this paper as Glessner et al., 2009
The broader protein family that includes CDH13 has been linked to ASD pathogenesis by CNV studies, homozygosity mapping, common variant findings, and the paper's pathway analysis.
“the larger family of proteins has been implicated in ASD pathogenesis through CNV studies (Glessner et al., 2009), homozygosity mapping (Morrow et al., 2008), common variant findings (Wang et al., 2009), and our pathway analysis (Figure 6)”
From Multiple recurrent de novo CNVs, including duplications of the 7q11.23 Williams syndrome region, are strongly associated with autism (2011) · cites this paper as Glessner et al., 2009
Pathway analyses have found ASD CNV enrichment in ubiquitin pathways, cellular proliferation/projection/motility and GTPase/Ras signaling, and synapse development/axon targeting/neuron motility.
“Glessner et al. (2009) observed an enrichment of CNVs at multiple sites, and some of their top hits were genes involved in ubiquitin pathways, including UBE3A, PARK2, RFWD2 and FBXO40. Pinto et al. (2010) observed an enrichment of CNVs within gene sets involved in cellular proliferation, projection and motility, and GTPase/Ras signaling. Gilman et al. (2011) found an enrichment of CNVs in gene”
From CNVs: Harbingers of a Rare Variant Revolution in Psychiatric Genetics (2012) · cites this paper as Glessner et al., 2009
The synaptic model predicted alterations in mRNA splicing and ubiquitination pathways that have since been identified.
“Interestingly, because many mRNA for synaptic genes are alternatively spliced, and the proteins regulated by ubiquitination, this paper was prescient in predicting alterations in mRNA splicing and ubiquitination pathways that have since been identified [49, 50].”
From Genetics of autism spectrum disorders (2011) · cites this paper as [50]
De novo mutations point to genes involved in synaptic function and localization, a pathway already suspected to be disrupted in ASD.
“de novo mutations also highlight the importance of genes with roles in synaptic function and localization – a pathway previously suspected to be disrupted in ASD [78].”
From A de novo convergence of autism genetics and molecular neuroscience (2014) · cites this paper as [78]
The two SHANK3 deletions reported by Glessner et al. (2009) in control subjects have not been validated and should be interpreted with caution.
“The two SHANK3 deletions reported by Glessner et al. (2009) [34] in control subjects have not been validated and should be interpreted with caution.”
From Meta-analysis of SHANK Mutations in Autism Spectrum Disorders: A Gradient of Severity in Cognitive Impairments (2014) · cites this paper as [34]
For controls, the two SHANK3 deletions reported by Glessner et al. (2009) among 2519 individuals were not validated and thus should be regarded with caution.
“For controls, the two SHANK3 deletions reported by Glessner et al. (2009) among 2 519 individuals, were not validated and thus should be regarded with caution.”
From Meta-analysis of SHANK Mutations in Autism Spectrum Disorders: A Gradient of Severity in Cognitive Impairments (2014) · cites this paper as Glessner et al. (2009)
Genetic mutations identified in small numbers of people with autism have been generated in mice.
“To incorporate construct validity for the various genetic mutations identified in small numbers of people with autism (12–21), these mutations have been generated in mice (22, 23).”
From Negative allosteric modulation of the mGluR5 receptor reduces repetitive behaviors and rescues social deficits in mouse models of autism (2012) · cites this paper as [18]
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“Of note, ubiquitin genes have been identified to cause autism (34).”
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- Authors
- Glessner, J. T., Wang, K., Cai, G., Korvatska, O., Kim, C. E., Wood, S., Zhang, H., Estes, A., Brune, C. W., Bradfield, J. P., Imielinski, M., Frackelton, E. C., Reichert, J., Crawford, E. L., Munson, J., Sleiman, P. M. A., Chiavacci, R., Annaiah, K., Thomas, K., Hou, C., Glaberson, W., Flory, J., Otieno, F., Garris, M., Soorya, L., Klei, L., Piven, J., Meyer, K. J., Anagnostou, E., Sakurai, T., Game, R. M., Rudd, D. S., Zurawiecki, D., McDougle, C. J., Davis, L. K., Miller, J., Posey, D. J., Michaels, S., Kolevzon, A., Silverman, J. M., Bernier, R., Levy, S. E., Schultz, R. T., Dawson, G., Owley, T., McMahon, W. M., Wassink, T. H., Sweeney, J. A., Nurnberger, J. I., Coon, H., Sutcliffe, J. S., Minshew, N. J., Grant, S. F. A., Bucan, M., Cook, E. H., Buxbaum, J. D., Devlin, B., Schellenberg, G. D., & Hakonarson, H.
- Affiliations
- Children's Hospital of Philadelphia (US)
- Icahn School of Medicine at Mount Sinai (US)
- University of Washington (US)
- University of Pittsburgh (US)
- University of Illinois Chicago (US)
- Vanderbilt University (US)
- University of North Carolina at Chapel Hill (US)
- University of Iowa (US)
- Indiana University Indianapolis (US)
- University of Utah (US)
- University of Pennsylvania (US)
- Corresponding author
- Schellenberg, Gerard D.
- Hakonarson, Hakon
- ORCID
- Glessner, Joseph T.
- Korvatska, Olena
- Zhang, Haitao
- Estes, Annette
- Imielinski, Marcin
- Munson, Jeffrey
- Thomas, Kelly
- Glaberson, Wendy
- Soorya, Latha
- Klei, Lambertus
- Piven, Joseph
- Meyer, Kacie J.
- Anagnostou, Evdokia
- Rudd, Danielle S.
- McDougle, Christopher J.
- Davis, Lea K.
- Kolevzon, Alexander
- Bernier, Raphael
- Levy, Susan E.
- Schultz, Robert T.
- Wassink, Thomas H.
- Sweeney, John A.
- Coon, Hilary
- Sutcliffe, James S.
- Minshew, Nancy J.
- Grant, Struan F. A.
- Cook, Edwin H.
- Buxbaum, Joseph D.
- Devlin, Bernie
- Schellenberg, Gerard D.
- Hakonarson, Hakon
- Venue
- Nature
- Published
- 2009-04-28
- Volume
- 459
- Issue
- 7246
- Pages
- 569-573
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC2925224
- OpenAlex
- W2073062083
- Cited by
- 1,421
- References
- 32
- Citations by year
- 2026: 27 · 2025: 35 · 2024: 36 · 2023: 45 · 2022: 53 · 2021: 43 · 2020: 118 · 2019: 67 · 2018: 56 · 2017: 70 · 2016: 74 · 2015: 91 · 2014: 125 · 2013: 128 · 2012: 137
- FWCI
- 72.23
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature (publishedVersion, public-domain)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- IUScholarWorks (Indiana University) (submittedVersion)
- Funders
- Autism Speaks
- U.S. Department of Veterans Affairs
- Children's Hospital of Philadelphia (UL1-RR-024134)
- Vanderbilt University
- University of Pennsylvania
- University of Washington
- University of Pittsburgh
- Health Research Board
- Cotswold Foundation
- University of Illinois at Urbana-Champaign
- University of North Carolina at Chapel Hill
- Vanderbilt Kennedy Center, Vanderbilt University Medical Center
- Medical Research Council
- National Institute of Mental Health (R01MH061009, U24MH081810, MH0666730, U54MH066673, MH69359, U10MH66766-02S1, R01MH069359, U10MH066766, MH 64547, R01MH057881, MH061009, R01MH064547)
- National Institute of General Medical Sciences (T32GM008629)
- National Institute of Neurological Disorders and Stroke (NS049261, R01NS049261)
- National Center for Research Resources (UL1-RR024134-03, UL1RR024134, M01RR000064)
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (P50HD055751, P50HD055782, P01HD035476, HD35476, HD055782-01, HD055751, U19HD035476)
- Topics
- Life Sciences › Neuroscience › Cognitive Neuroscience › Autism Spectrum Disorder Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetics and Neurodevelopmental Disorders
- Keywords
- autism spectrum disorder, copy number variation, genetic susceptibility, neuronal cell adhesion molecule, cadherins, ubiquitin pathway, neuroligin-1, ASTN2, UBE3A, PARK2, single nucleotide polymorphisms, neurodevelopmental disorders, gene-environment interaction
- MeSH terms
- Autistic Disorder, Europe, Genotype, Humans, Neurons, Genetic Variation, Reproducibility of Results, Cohort Studies, Cell Adhesion Molecules, Neuronal, Genome, Human, Case-Control Studies, Polymerase Chain Reaction, Gene Dosage, Genetic Predisposition to Disease, Polymorphism, Single Nucleotide, Ubiquitin, Gene Regulatory Networks
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