Chromosome microarray analysis is now considered a first-tier test for individuals with intellectual disability and ASDs.1
It has been suggested that the detection rate using high-resolution chromosome microarrays among unexplained cases of intellectual disabilities and neurodevelopmental or neuropsychiatric phenotypes is between 7 and 20%,27
depending on the cohort. Exon-targeted microarrays, with increased density of coverage within the coding regions of disease-associated genes, may further increase this diagnostic yield.25
We report a total of 24 cases of intragenic NRXN1
deletions, with deletion sizes varying between 17 and 913
Deletions and loss-of-function point mutations of NRXN1
have been linked to autism, schizophrenia and intellectual disability.13, 14, 15, 21, 23
More recently, intragenic rearrangements of NRXN1
have been described and associated with a wide spectrum of developmental disorders.23, 24
There is a significantly higher prevalence of NRXN1
deletions among clinical samples when compared with control populations. In the reported cohort, the incidence of intragenic NRXN1
deletions was 20/8051 among clinically referred cases (0.25%), which is quasi identical to the rate reported by Ching et al
(9/3450; ie, 0.25%).24
The frequency of exonic deletions of NRXN1-α
among control populations is 10/51
Similar findings have been reported for schizophrenia populations, where incidence of NRXN1
kb among individuals with schizophrenia has been determined 0.19% (17/8798) vs
054) among controls.13
The largest previously reported cohort of individuals with NRXN1
deletions includes nine individuals with whole-gene or multiple exon deletions, and three individuals with deletions in intron 5. In that cohort, the most common symptoms included cognitive impairment (5/12), language delay (9/12), ASDs (5/12) and hypotonia (4/12).24
Although multiple publications suggest NRXN1
deletions to be pathogenic, little is known about the prevalence and pathogenicity of NRXN1
duplications or about intronic CNVs in the NRXN1
gene. Intragenic, frame-shifting duplications would represent an exception, but only one such case has been described.23
No genotype–phenotype correlations for NRXN1
CNVs have been suggested, likely due to the fairly small number of cases identified.
Here, we describe the largest cohort of individuals with intragenic deletions of NRNX1
reported to date, provide detailed clinical and phenotypic information, and, for the first time, propose some genotype–phenotype correlation for exonic NRXN1
deletions. Similar to previous reports, developmental delay and intellectual disability (12/13), ASDs (10/17) and hypotonia (8/17) represent some of the most common phenotypes observed among those with exonic deletions of NRXN1
. In addition, attention deficit hyperactivity disorder (ADHD) is reported in 7 of 17 patients. The inheritance of the reported exonic deletion cases was delineated in 12 independent cases. Of these, 3 (25%) were found to be de novo.
In a large meta-analysis, Rees et al28
calculated the de novo
rate of exonic NRXN1
deletions to 22%, which is remarkably similar.
Previously, in four studies, a total of seven individuals with NRXN1
deletions were reported to have a history of seizures. One was an individual with a whole-gene deletion of NRXN1
Gregor et al29
reported a total of six heterozygous intragenic NRXN1
deletions, three of which had seizures. However, one of their patients (N4) had additional CNVs at 15q26 (deletion) and 16q12 (duplication), and another proband (N5) was the offspring of a consanguineous mating. In a different study, a NRXN1
deletion carrier was reported to have had one single seizure as a child.21
Lastly, Harrison et al30
recently reported on two sisters with compound heterozygous deletions of NRXN1
(one affecting the promoter and exons 1–5, and the second one deleting exons 20 and 21). Both sisters had severe, early-onset epilepsy.
In our study, 9 of 17 patients are affected with epilepsy or have a history of seizures. Four individuals have absence seizures, and five have generalized tonic–clonic epilepsy. Most interestingly, epilepsy is a consistent feature of individuals with C-terminal intragenic deletions. Only 2 of 10 individuals with N-terminal deletions (within the first five exons of NRNX1
) were reported to have a history of seizures, while all seven patients with C-terminal deletions have epilepsy. One might speculate that this is because of C-terminal deletions affecting other neurexin 1 isoforms, considering the extensive use of alternative splicing, which has been reported for the neurexin genes.31
Notably, within this given cohort, all four patients with deletions affecting NRXN1-β
(patients E14–E17) have epilepsy.
A second phenotype associated with C-terminal deletions, but not with N-terminal deletions of NRXN1, is macrocephaly. Comparing the head sizes of all 17 individuals with exonic deletions, there is a significant difference in head size. Defining macrocephaly as a head circumference at or above the 95th percentile for age, five of seven patients with C-terminal deletions are affected, whereas none of the individuals with N-terminal deletions meets this criterion.
Future studies will show whether these genotype–phenotype correlations are consistent across various cohorts. As for most, if not all, neuropsychiatric disorders associated with CNVs, there is considerable variability of expressivity of symptoms, and only larger cohorts will uncover strong genotype–phenotype relationships.
Detailed molecular studies would be warranted to unravel how certain exonic deletions may affect various splice forms of the neurexin proteins and how that affects neuronal connectivity, excitability and function.
Our study leaves the question of whether intronic deletions of NRXN1 may be pathogenic unanswered. One could imagine that certain intronic deletions affect splicing or delete promoter sequences of respective isoforms. However, none of the intronic deletions reported herein affects known splice sites or promoter sequences of neurexin 1 (NRXN1) isoforms. Furthermore, all seven cases of intronic NRXN1 deletions are inherited (except for one, for which the father is not available for study), and of the six carrier parents, only one is reported to manifest neuropsychiatric symptoms (anxiety and depression). This may suggest that intronic deletions of NRXN1 are not pathogenic per se, or at least with relatively low penetrance, operating in a multi-factorial milieu to increase risk for developmental and neuropsychiatric phenotypes.
In summary, we report the clinical and molecular phenotypes of 24 patients with intragenic CNVs of the NRXN1 gene. Exonic deletions of NRXN1 are associated with developmental delay, intellectual disability of various degrees, ASDs, hypotonia and ADHD. Deletions of C-terminal exons of NRXN1 associate with increased head size and epilepsy within our cohort.