CNTN6 mutations are risk factors for abnormal auditory sensory perception in autism spectrum disorders

Abstract

Contactin genes CNTN5 and CNTN6 code for neuronal cell adhesion molecules that promote neurite outgrowth in sensory-motor neuronal pathways. Mutations of CNTN5 and CNTN6 have previously been reported in individuals with autism spectrum disorders (ASDs), but very little is known on their prevalence and clinical impact. In this study, we identified CNTN5 and CNTN6 deleterious variants in individuals with ASD. Among the carriers, a girl with ASD and attention-deficit/hyperactivity disorder was carrying five copies of CNTN5. For CNTN6, both deletions (6/1534 ASD vs 1/8936 controls; P=0.00006) and private coding sequence variants (18/501 ASD vs 535/33480 controls; P=0.0005) were enriched in individuals with ASD. Among the rare CNTN6 variants, two deletions were transmitted by fathers diagnosed with ASD, one stop mutation CNTN6^W923X was transmitted by a mother to her two sons with ASD and one variant CNTN6^P770L was found de novo in a boy with ASD. Clinical investigations of the patients carrying CNTN5 or CNTN6 variants showed that they were hypersensitive to sounds (a condition called hyperacusis) and displayed changes in wave latency within the auditory pathway. These results reinforce the hypothesis of abnormal neuronal connectivity in the pathophysiology of ASD and shed new light on the genes that increase risk for abnormal sensory perception in ASD.

Figure 1

Families carrying CNTN5 (a) and CNTN6 (b) exonic CNVs or rare SNVs. CNTN5 and CNTN6 CNVs and SNVs are represented by dots. Black-filled symbols indicate a diagnosis of ASD with intellectual disability, whereas gray-filled symbols indicate a diagnosis of ASD without intellectual disability. In multiplex families, an arrow indicates the proband. Based on the ADI-R and clinical examination, normal (green) or abnormal (red) hypersensitivity to sounds and motor coordination ability are indicated by a schematic ear and hand, respectively. The absence of ear/hand means that information was not available. The locations of all CNVs identified in this study are indicated (hg19) and shown in Supplementary Figures 2 and 3. All families with CNTN5- or CNTN6-coding SNVs are shown in Supplementary Figure 4. ASD, autism spectrum disorder; CNV, copy-number variants; SNV, single-nucleotide variants.

Figure 2

Frequency of CNTN5 and CNTN6 exonic CNVs and rare SNVs identified in patients with ASD and in controls. Differences in frequency of carriers of CNTN5 or CNTN6 CNVs or SNVs between patients and controls were calculated using a Fischer's exact test. The rare SNVs were defined as in Murdoch et al.: seen in either cases or controls exclusively, missense, nonsense, splice site, or start or stop codon disruptions with a frequency of less than 1% in the general European (Non-Finnish) population from ExAC (http://exac.broadinstitute.org/). ASD, autism spectrum disorder; CNV, copy-number variants; SNV, single-nucleotide variants.

Figure 3

Functional impact of the CNTN6 variants. The predicted scores from five prediction algorithms are shown as a gradient for each mutation. The effect of each variant on neurite length, on the structure of the CNTN6 protein and the clinical observation of hypersensitivity to sounds (hyperacusis) are also indicated. The Divided squares represent multiple autism spectrum disorder (ASD) individuals carrying the same mutation. Missing squares represent unavailable information. The star indicates a de novo mutation.

Figure 4

Clinical investigation and auditory brainstem responses in CNTN5 or CNTN6 rare variant carriers and non-carriers. (a) Individuals with ASD carrying CNTN5 (N=24) or CNTN6 (N=24) rare variants are more prone to suffer from hyperacusis or to display abnormal idiosyncratic-negative response to specific sensory stimuli than the rest of the cohort of patients with ASD (N=544). (b) Auditory brain response in the probands carrying CNTN5 or CNTN6 rare variants, and their first-degree relatives. The graph represents response latencies (in milliseconds) for waves I, III and V as a function of signal intensity (in decibels) in right ear (green dots) and left ear (red dots). Normal ranges of response (5–95th percentile) are shown in yellow (based on manufacturer information); variants of individuals outside the normal range are indicated. Electrodes were placed at Fz, ipsilateral earlobe and contralateral earlobe (ground). Responses were amplified with a gain of 100 000 and digitally filtered with a bandwidth of 100–3000 Hz. Each ear was stimulated by alternating 60 and 80 dB clicks with a presentation rate of 29 per second. Clicks were delivered using Etymotic Research ER-3 insert earphones. Two separate recordings that included 2000 individual sweeps were averaged. ASD, autism spectrum disorder.