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Molecular Genetics of Neurodevelopmental Disorders: 2nd Edition
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Molecular Genetics of Neurodevelopmental Disorders: 2nd Edition

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Human Genomics and Genetic Diseases".

Deadline for manuscript submissions: 25 January 2026 | Viewed by 824

Special Issue Editors

Prof. Dr. Richard Eugene Frye

E-Mail Website
Guest Editor
Autism Discovery and Treatment Foundation and Rossignol Medical Center, Phoenix, AZ, USA
Interests: neurodevelopmental disorders; metabolic disorders; genetic symptoms; epigenetics; gene regulation
Special Issues, Collections and Topics in MDPI journals
Dr. Richard Boles

E-Mail Website
Guest Editor
Mitochondrial and Molecular Medicine, 630 S Raymond Avenue, Unit 310, Pasadena, CA 91105, USA
Interests: mitochondrial medicine; functional disease (including cyclic vomiting syndrome, other atypical forms of migraine, and chronic fatigue syndrome); autism spectrum disorders
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Following the success of our first edition, we are delighted to present the second edition of this Special Issue, continuing our exploration of neurodevelopmental disorders—a group of conditions that profoundly impact children during critical developmental periods, with lifelong consequences for them and their families. Despite significant research, key questions remain regarding the etiology of these disorders. While genetic factors play a key role and numerous risk variants are known, the mechanisms linking these variants to autism phenotypes—as well as how interventions might alter developmental trajectories—are still unclear.

This second edition aims to publish high-impact, cutting-edge articles on emerging developments in complex genetic processes and/or gene–environmental interactions, which can provide insight into the pathophysiological processes that underlie the etiology or pathophysiology of neurodevelopmental disorders.

We encourage the submission of manuscripts describing any of the above-listed factors that provide insight into the etiological or pathophysiological processes underlying neurodevelopmental disorders. Research that enhances the description of genetic variants or conditions and elucidates underlying biological mechanisms and concepts that translate into novel treatments is also encouraged but not required.

Manuscripts will be considered that describe any genetic processes or genetic syndromes involved in the development of neurodevelopmental disorders.

Prof. Dr. Richard Eugene Frye
Dr. Richard Boles
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • neurodevelopmental disorders
  • attention deficit hyperactivity disorder
  • intellectual disabilities
  • autism spectrum disorder
  • mitochondria
  • neuroinflammation
  • epigenetics
  • transcriptomics
  • genetic syndromes
  • polygenetic interactions

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Published Papers (1 paper)

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Research

36 pages, 369 KB  
Article
De Novo Variants Predominate in Autism Spectrum Disorder
by Richard G. Boles, Omri Bar, Philip T. Boles, Zoë R. Hill and Richard E. Frye
Genes 2025, 16(9), 1099; https://doi.org/10.3390/genes16091099 - 17 Sep 2025
Viewed by 359
Abstract
Background: Autism spectrum disorder (ASD) is a common condition with substantial personal and financial burdens of lifelong implication. Multiple twin studies have confirmed a genetic or inherited component at ~80%, higher than any other common condition. However, ASD’s rapidly accelerating prevalence, now at [...] Read more.
Background: Autism spectrum disorder (ASD) is a common condition with substantial personal and financial burdens of lifelong implication. Multiple twin studies have confirmed a genetic or inherited component at ~80%, higher than any other common condition. However, ASD’s rapidly accelerating prevalence, now at 1 in 31 in the USA, appears to defy a predominantly genetic basis and implicate our rapidly changing environment. A potential explanation for this paradox is a recent increase in de novo variants (DNVs), which are “new” mutations present in the patient yet absent in both parents. The present authors recently reported using trio whole-genome sequencing (trio-WGS) that DNVs highly likely to be highly disease-associated (“Principal Diagnostic Variants”, PDVs), mostly missense variants, were present in (25/50) 50% of the ASD patients clinically evaluated by our team. Methods: The current study was designed to support this observation with trio-WGS in 100 additional unrelated ASD patients. Results: De novo PDVs were identified in 47/100 (47%) of cases, in close approximation to our previous work. Using non-transcribed (up and downstream) variants for all genes as a control group, these DNV-PDVs were far more likely (p < 0.0001, OR 5.8, 95% C.I. 2.9–11) to be in SFARI-listed genes associated with ASD. Consistent with the emerging polygenic model, using the same analyses, inherited missense variants were also associated with ASD (p < 0.0001). Highly unexpectedly, silent variants, both inherited (p < 0.0001) and de novo (p < 0.007), were also statistically associated with ASD, and, among inherited variants, silent variants were more associated with ASD than were missense variants (p < 0.0001). Adding silent DNVs as PDVs increases the proportion of our subjects with at least one DNV-PDV to 55% of the subjects. Conclusions: Our proposed model for ASD, with prominent DNVs in most that are genetic yet not inherited, predicts the known predominant genetic pathogenesis and the accelerating prevalence of ASD, possibly from environmental factors, including insufficient nutrients and toxicant exposures, and/or the disrupted folate metabolism known to be associated with ASD. Limitations to this study include predominant inclusion of severely affected individuals and the lack of an unaffected control group and functional validation of variant pathogenicity. Full article
(This article belongs to the Special Issue Molecular Genetics of Neurodevelopmental Disorders: 2nd Edition)
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