Comprehensive cross-disorder analyses of CNTNAP2 suggest it is unlikely to be a primary risk gene for psychiatric disorders

Abstract

The contactin-associated protein-like 2 (CNTNAP2) gene is a member of the neurexin superfamily. CNTNAP2 was first implicated in the cortical dysplasia-focal epilepsy (CDFE) syndrome, a recessive disease characterized by intellectual disability, epilepsy, language impairments and autistic features. Associated SNPs and heterozygous deletions in CNTNAP2 were subsequently reported in autism, schizophrenia and other psychiatric or neurological disorders. We aimed to comprehensively examine evidence for the role of CNTNAP2 in susceptibility to psychiatric disorders, by the analysis of multiple classes of genetic variation in large genomic datasets. In this study we used: i) summary statistics from the Psychiatric Genomics Consortium (PGC) GWAS for seven psychiatric disorders; ii) examined all reported CNTNAP2 structural variants in patients and controls; iii) performed cross-disorder analysis of functional or previously associated SNPs; and iv) conducted burden tests for pathogenic rare variants using sequencing data (4,483 ASD and 6,135 schizophrenia cases, and 13,042 controls). The distribution of CNVs across CNTNAP2 in psychiatric cases from previous reports was no different from controls of the database of genomic variants. Gene-based association testing did not implicate common variants in autism, schizophrenia or other psychiatric phenotypes. The association of proposed functional SNPs rs7794745 and rs2710102, reported to influence brain connectivity, was not replicated; nor did predicted functional SNPs yield significant results in meta-analysis across psychiatric disorders at either SNP-level or gene-level. Disrupting CNTNAP2 rare variant burden was not higher in autism or schizophrenia compared to controls. Finally, in a CNV mircroarray study of an extended bipolar disorder family with 5 affected relatives we previously identified a 131kb deletion in CNTNAP2 intron 1, removing a FOXP2 transcription factor binding site. Quantitative-PCR validation and segregation analysis of this CNV revealed imperfect segregation with BD. This large comprehensive study indicates that CNTNAP2 may not be a robust risk gene for psychiatric phenotypes.

Fig 1. Overview of heterozygous CNVs spanning the CNTNAP2 gene across several diseases.

Abbreviations: ID (Intellectual disability), ASD (autism spectrum disorder), SCZ (schizophrenia), BD (bipolar disorder), ADHD (Attention-deficit/hyperactivity disorder), EP (epilepsy), TS (Tourette syndrome), CMT2 (axonal Charcot-Marie-Tooth), and SS (Speech spectrum: speech delay, childhood apraxia of speech and dyslexia). In parenthesis is reported the reference to each study. *, additional rearrangements reported in this patient. The dashed lines represent the exons and the upper box shows the position of the FOXP2 binding site. In dark shading, CNVs≥80kb found in the general populations from the Database of Genomic Variants are shown.

Fig 2. CNV deletion encompassing intron 1 of CNTNAP2 in an extended family with bipolar disorder.

A) CytoScan HD array output image shows the position of the drop in signal intensity of 340 probes, indicating a deletion spanning 131kb (chr7:146203548–146334635; GRCh37/hg19) found in the patient 8401. The position of the FOXP2 binding site within the deletion is shown above. B) The bipolar pedigree includes five patients with bipolar disorder I (BPI) across two generations. Symbols: _, individuals with DNA available; &, individuals with whole exome data; #, individuals analysed for genome-wide CNVs through the CytoScan HD array; blue squares, individuals included in CNV qPCR validation and genotyping analysis, for which heterozygous deletion carriers are indicated as “+/del” and non-carriers are indicated as “+/+”. Inferred genotypes are in parentheses. C) Gene dosage results of the qPCR experiments validating the deletion in patient 8401, and showing the deletion in unaffected subject 8407.