Rare deleterious mutations of the gene EFR3A in autism spectrum disorders

Abha R Gupta; Michelle Pirruccello; Feng Cheng; Hyo Jung Kang; Thomas V Fernandez; Jeremy M Baskin; Murim Choi; Li Liu; Adife Gulhan Ercan-Sencicek; John D Murdoch; Lambertus Klei; Benjamin M Neale; Daniel Franjic; Mark J Daly; Richard P Lifton; Pietro De Camilli; Hongyu Zhao; Nenad Sestan; Matthew W State

doi:10.1186/2040-2392-5-31

Rare deleterious mutations of the gene EFR3A in autism spectrum disorders

Mol Autism. 2014 Apr 29:5:31. doi: 10.1186/2040-2392-5-31. eCollection 2014.

Authors

Abha R Gupta¹, Michelle Pirruccello², Feng Cheng³, Hyo Jung Kang⁴, Thomas V Fernandez⁵, Jeremy M Baskin⁶, Murim Choi⁷, Li Liu⁸, Adife Gulhan Ercan-Sencicek⁹, John D Murdoch¹⁰, Lambertus Klei¹¹, Benjamin M Neale¹², Daniel Franjic¹³, Mark J Daly¹², Richard P Lifton⁷, Pietro De Camilli⁶, Hongyu Zhao¹⁴, Nenad Sestan¹³, Matthew W State¹⁵

Affiliations

¹ Department of Pediatrics and Child Study Center, Yale School of Medicine, New Haven, CT 06520, USA.
² Scholar Rock, LLC, 300 Third Street, 4th floor, Cambridge, MA 02142, USA.
³ Department of Neurobiology, Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06520, USA ; College of Pharmacy, University of South Florida, Tampa, FL 33612, USA.
⁴ Department of Neurobiology, Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06520, USA ; Department of Life Science, Chung-Ang University, Seoul, Korea.
⁵ Department of Psychiatry and Child Study Center, Yale School of Medicine, New Haven, CT 06520, USA.
⁶ Department of Cell Biology, Howard Hughes Medical Institute, Program in Cellular Neuroscience Neurodegeneration and Repair, Yale School of Medicine, New Haven, CT 06520, USA.
⁷ Department of Genetics, Howard Hughes Medical Institute, Yale School of Medicine, New Haven, CT 06520, USA.
⁸ Department of Statistics, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
⁹ Program on Neurogenetics, Child Study Center, Yale School of Medicine, New Haven, CT 06520, USA.
¹⁰ Program on Neurogenetics, Child Study Center, Department of Psychiatry, Department of Genetics, Yale School of Medicine, New Haven, CT 06520, USA.
¹¹ Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA.
¹² Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
¹³ Department of Neurobiology, Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06520, USA.
¹⁴ Departments of Biostatistics and Genetics, Yale School of Medicine, New Haven, CT 06520, USA.
¹⁵ Department of Psychiatry, University of California San Francisco, San Francisco, CA 94143, USA.

Abstract

Background: Whole-exome sequencing studies in autism spectrum disorder (ASD) have identified de novo mutations in novel candidate genes, including the synaptic gene Eighty-five Requiring 3A (EFR3A). EFR3A is a critical component of a protein complex required for the synthesis of the phosphoinositide PtdIns4P, which has a variety of functions at the neural synapse. We hypothesized that deleterious mutations in EFR3A would be significantly associated with ASD.

Methods: We conducted a large case/control association study by deep resequencing and analysis of whole-exome data for coding and splice site variants in EFR3A. We determined the potential impact of these variants on protein structure and function by a variety of conservation measures and analysis of the Saccharomyces cerevisiae Efr3 crystal structure. We also analyzed the expression pattern of EFR3A in human brain tissue.

Results: Rare nonsynonymous mutations in EFR3A were more common among cases (16 / 2,196 = 0.73%) than matched controls (12 / 3,389 = 0.35%) and were statistically more common at conserved nucleotides based on an experiment-wide significance threshold (P = 0.0077, permutation test). Crystal structure analysis revealed that mutations likely to be deleterious were also statistically more common in cases than controls (P = 0.017, Fisher exact test). Furthermore, EFR3A is expressed in cortical neurons, including pyramidal neurons, during human fetal brain development in a pattern consistent with ASD-related genes, and it is strongly co-expressed (P < 2.2 × 10(-16), Wilcoxon test) with a module of genes significantly associated with ASD.

Conclusions: Rare deleterious mutations in EFR3A were found to be associated with ASD using an experiment-wide significance threshold. Synaptic phosphoinositide metabolism has been strongly implicated in syndromic forms of ASD. These data for EFR3A strengthen the evidence for the involvement of this pathway in idiopathic autism.

Keywords: Autism spectrum disorder; EFR3A; Genetics; Phosphoinositide metabolism; Rare variants; Synapse.

Abstract

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