The recent recognition of genomic imbalance in many chromosomal regions that are associated with autism, mental retardation and schizophrenia is due to the increasing use of whole genome high resolution array CGH in the evaluation of individuals with these disorders. Our clinical subjects with NRXN1 deletion were ascertained through a patient population presenting with a broad range of referring diagnoses.
Through a careful review of medical records, we identified in our subjects a number of clinical features that had not been previously associated with NRXN1 deletions. These include language delays, mental retardation without autism, hypotonia, and hemangiomas.
In addition, two of our subjects (5, 12) had ventricular septal defects. Interestingly, the human cDNA homologous to rat NRXN1
-α has been isolated in both brain and heart tissues suggesting a potential role for Neurexin1 in both brain and heart development [Nagase et al. 1998
]. One of these subjects (5) also had evidence of multiple congenital anomalies including vertebral anomalies in the form of a VACTERL association. Vertebral anomalies have also been reported in one other case in the literature [Zahir et al. 2008
A previous report showed the presence of a seizure disorder in two unrelated individuals sharing the same missense variant in exon 1 of NRXN1
- β [Feng et al. 2006
]. In our cohort, only one subject had a seizure disorder (subject 1), although his 5 Mb deletion encompassed the entire NRXN1
gene as well as the genes for follicle-stimulating hormone receptor (FSHR
), luteinizing hormone/choriogonadotropin receptor (LHCGR
), and Stoned B
-like factor (STN1
). To our knowledge, none of these genes has been associated with seizures or mental retardation in the literature.
Although we cannot be certain that these features are a direct consequence of NRXN1 deletion, our observations suggest that the phenotypic characteristics of NRXN1 deletion may be wider than previously reported.
The mutations we have observed in our clinical cohort are primarily in NRXN1-α. Subjects with small deletions (under 3 Mb) clustered into two groups (). One group (subjects 3-7) had deletions involving part of the initial LNS and EGF domains-encoding regions of NRXN1-α. Of these 5 individuals, 3 had autism spectrum disorders. One additional case from the Homozygosity Mapping Collaborative for Autism was also found to have a deletion in this region, which is similar to the deletion in subject 7 from the clinically referred cohort.
A second group (subjects 8-12) had deletions that clustered around a region further from the α promotor of the gene (). All 5 of these subjects’ deletions encompassed an exon of an isoform whose function is not well understood. Furthermore, while 2 subjects (8, 9) had deletions involving other exons of NRXN1-α as well as this minor isoform, 3 subjects’ deletions (10-12) contain only the exon of this minor isoform. This minor isoform is an Ensembl annotated transcript, named ENST00000406859 (). It contains 13 exons with 2,590 basepairs transcription and 856 residues of translation length. The coded protein (ENSP00000385681) consists of one LNS and EGF domain. Its function is currently unknown.
One such subject (10) with a de novo deletion in this region has been diagnosed with Pervasive Developmental Disorder-Not Otherwise Specified, suggesting potential clinical relevance for this isoform. This deletion in intron 5 has not to our knowledge been previously reported as being associated with abnormal development.
Neurexin 1-beta mutations were less common. Two of the subjects in our cohort had large deletions encompassing exons for NRXN1
-α and β. Missense variants in NRXN1
-β (R8P, L13F, S14L, and T40S) have previously been identified in individuals with autism [Feng et al. 2006
; Kim et al. 2008
]. Relatives of these individuals with autism who shared these missense mutations demonstrated some degree of learning or behavioral issues but did not appear to meet full autism spectrum disorder criteria [Feng et al. 2006
; Kim et al. 2008
]. This is consistent with our findings of a mixed phenotype associated with deletions in this region ranging from autism spectrum disorders to hypotonia with carrier relatives who are not as affected.
In addition to their NRXN1 deletions, subjects 8 and 11 had additional genomic imbalances as described in . These genomic imbalances were all inherited from unaffected parents. The two duplications on 15q26.3 and 17p11.2 in subject 11 overlap with known benign CNVs and are unlikely contributory factors to the patient’s condition. The duplication at 5p13.2 in subject 11 and deletion at 3p24.3 in subject 8 are not previously reported CNV but contain no known genes associated with developmental disorders, thus are considered as CNV of unknown significance. Nevertheless, it is unclear whether these CNVs modified the observed phenotype.
NRXN1 and Synapse Function
The function of NRXN1
in facilitating synaptic transmission suggests that mutations in this gene may predispose to a neurologic disconnection syndrome. Long range disconnections between neural networks have been hypothesized to be causative in some populations with autism [Barnea-Goraly et al. 2004
; Frith 2004
; Geschwind and Levitt 2007
; Just et al. 2004
]. The effects of NRXN1
on language development and hypotonia may likewise be related to long range connectivity within the brain.
Phenotypic variations may reflect the highly pleiotropic effects observed for specific CNVs such as associated with NRXN1. In addition, a number of our subjects inherited NRXN1 deletions from their parents. The detailed phenotype of these parents were not described in the medical records except in the family history, but the parents were ostensibly less affected than their children. This suggests that deletion in the NRXN1 gene may not be fully penetrant, or interacts with other genes resulting in the variable phenotype. Further research efforts to investigate such variable phenotypes associated with this unstable genomic region will provide further insight into the role of NRXN1 in the development of language delays, autism spectrum disorders and physical features.
The accuracy and completeness of the clinical phenotype identified in this study is entirely dependent on the clinical information that was documented in the medical records of these subjects, often before the NRXN1 deletions were identified in them. Because of the clinical variability exhibited in our cohort, the subjects were seen by a variety of specialists, which affected the completeness of data.
In addition, the parents were not formally assessed to ascertain their cognitive, physical and behavioral phenotypes. As noted above, review of family history suggests that some parents may have shared similar phenotypes to their children. We are conducting further testing on both the subjects and their parents to better clarify developmental and/or social cognition issues in subjects and their parents.
For the deletion CNV significance test, we used the normal control data generated by different genomic profiling array platforms as reference. Knowing that the sensitivity and specificity differ from one array platform to another, this may not be an optimal comparison. However, the effort was made to minimize the detection bias between different array platforms. Here we have only chosen recent studies using array platform of similar resolution as ours. All these published papers reported the detection of smaller CNV, suggesting that technically all these array platforms were able to detect any CNV identified in this study. Thus this comparison, although an approximation, is on the conservative side.
Finally we acknowledge that while our clinically ascertained subjects were not drawn from a cohort with a single diagnosis such as autism or schizophrenia, they were ascertained from a heterogeneously affected group in whom genetic testing was considered clinically relevant. As a result, there is ascertainment bias and our findings may not reflect the true distribution of physical and developmental findings in the NRXN1 deletion phenotype. Nevertheless, we have demonstrated that there are a number of other phenotypic features present in this clinical population beyond what has previously been identified in the literature.