An increased burden of rare exonic variants in NRXN1 microdeletion carriers is likely to enhance the penetrance for autism spectrum disorder

Abstract

Autism spectrum disorder (ASD) is characterized by a complex polygenic background, but with the unique feature of a subset of cases (~15%-30%) presenting a rare large-effect variant. However, clinical interpretation in these cases is often complicated by incomplete penetrance, variable expressivity and different neurodevelopmental trajectories. NRXN1 intragenic deletions represent the prototype of such ASD-associated susceptibility variants. From chromosomal microarrays analysis of 104 ASD individuals, we identified an inherited NRXN1 deletion in a trio family. We carried out whole-exome sequencing and deep sequencing of mitochondrial DNA (mtDNA) in this family, to evaluate the burden of rare variants which may contribute to the phenotypic outcome in NRXN1 deletion carriers. We identified an increased burden of exonic rare variants in the ASD child compared to the unaffected NRXN1 deletion-transmitting mother, which remains significant if we restrict the analysis to potentially deleterious rare variants only (P = 6.07 × 10^-5 ). We also detected significant interaction enrichment among genes with damaging variants in the proband, suggesting that additional rare variants in interacting genes collectively contribute to cross the liability threshold for ASD. Finally, the proband's mtDNA presented five low-level heteroplasmic mtDNA variants that were absent in the mother, and two maternally inherited variants with increased heteroplasmic load. This study underlines the importance of a comprehensive assessment of the genomic background in carriers of large-effect variants, as penetrance modulation by additional interacting rare variants to might represent a widespread mechanism in neurodevelopmental disorders.

Keywords: NRXN1; ASD; mtDNA; penetrance; rare variants.

Figure 1

NRXN1 deletion in the ASD proband. A, UCSC hg19 screenshot showing the NRXN1 maternally inherited deletion detected by array CGH in the female proband and validated by qPCR in the family. qPCR probes used for validation and inheritance testing are shown in green. B, Schematic representation outlining domains structure of neurexin alpha and neurexin beta protein variants. Canonical splice sites (SS) of neurexins are indicated by arrows. Protein region affected by deletion is highlighted in red

Figure 2

STRING network of predicted protein‐protein interactions for genes harbouring LGD or likely damaging missense variants identified by WES in the female proband. The network of predicted NRXN1 associations has been magnified. The edges represent the predicted functional associations and line colour indicates the type of interaction evidence: Red line—presence of fusion evidence; Green line—neighbourhood evidence; Blue line—cooccurrence evidence; Purple line—experimental evidence; Yellow line—text‐mining evidence; Light blue line—database evidence; Black line—co‐expression evidence. NRXN1 and CNTNAP5 show homology, co‐expression and text‐mining interaction evidence; NRXN1 and KIRREL2 show text‐mining interaction evidence; NRXN1 and NCAN show co‐expression and text‐mining interaction evidence; NRXN1 and TULP1 show co‐expression and experimental interaction evidence

Figure 3

Multi‐factorial threshold model for ASD in this family. Each family member has an ASD risk cup with balls representing risk variants that contribute to ASD with variable degrees of impact. In both parents, the burden of risk variants is not enough to develop ASD, while in the child the ASD threshold is reached as a combination of strong and weak, inherited and de novo genetic variants. The NRXN1 deletion is depicted as a strong, primary contributing factor to reaching the ASD threshold in the ASD child, but not sufficient alone to develop ASD in the deletion carrier mother ⁵⁷