The clinical significance of small copy number variants in neurodevelopmental disorders

Abstract

Background: Despite abundant evidence for pathogenicity of large copy number variants (CNVs) in neurodevelopmental disorders (NDDs), the individual significance of genome-wide rare CNVs <500 kb has not been well elucidated in a clinical context.

Methods: By high-resolution chromosomal microarray analysis, we investigated the clinical significance of all rare non-polymorphic exonic CNVs sizing 1-500 kb in a cohort of 714 patients with undiagnosed NDDs.

Results: We detected 96 rare CNVs <500 kb affecting coding regions, of which 58 (60.4%) were confirmed. 6 of 14 confirmed de novo, one of two homozygous and four heterozygous inherited CNVs affected the known microdeletion regions 17q21.31, 16p11.2 and 2p21 or OMIM morbid genes (CASK, CREBBP, PAFAH1B1, SATB2; AUTS2, NRXN3, GRM8). Two further de novo CNVs affecting single genes (MED13L, CTNND2) were instrumental in delineating novel recurrent conditions. For the first time, we here report exonic deletions of CTNND2 causing low normal IQ with learning difficulties with or without autism spectrum disorder. Additionally, we discovered a homozygous out-of-frame deletion of ACOT7 associated with features comparable to the published mouse model. In total, 24.1% of the confirmed small CNVs were categorised as pathogenic or likely pathogenic (median size 130 kb), 17.2% as likely benign, 3.4% represented incidental findings and 55.2% remained unclear.

Conclusions: These results verify the diagnostic relevance of genome-wide rare CNVs <500 kb, which were found pathogenic in ∼2% (14/714) of cases (1.1% de novo, 0.3% homozygous, 0.6% inherited) and highlight their inherent potential for discovery of new conditions.

Keywords: Clinical Genetics; Copy-Number; Developmental; Diagnostics; Genome-Wide.

Figure 1

Comparison between true versus false positive status of small copy number variants (CNVs) detected by chromosomal microarray analysis (CMA) and their size, confidence value, marker count and marker count per kb. (A) False positive CNVs were significantly smaller in size (3–181 kb, median 19 kb, mean 45.3 kb) than true CNVs (2–492 kb, median 131 kb, mean 164.7 kb) (p<0.0001). (B) There was also a significant difference between the two groups regarding their confidence values (mean of 88.9% vs 91.9%, p<0.0001) and (C) marker count (median of 20 vs 96, mean of 39.9 vs 163.8, p<0.0001). (D) No significant difference was observed for the marker count per kb within the CNV (1.5±1.14 vs 1.1±0.67, p=0.1).

Figure 2

Schematic representation of CTNND2 deletions detected in patients. Patient 1 (DECIPHER #284528) with a de novo deletion of exons 4–7, patient 2 (DECIPHER #248402) with a paternally inherited deletion encompassing exons 2–8, patient 3 (DECIPHER #269928) with a maternally inherited deletion of exons 1–3 and 5'UTR and patient 4 (DECIPHER #271234) with a maternally inherited deletion of exon 3.

Figure 3

Structure of the Satb2 tetramerisation domain and upper incisors in the patient with intragenic SATB2 duplication. (A) The four subunits of the tetramer are shown in different colours and those parts, which are duplicated in the mutant, are shown in space-filled presentation. This duplication will affect the interfaces between the dimers that form the tetramer (black arrows). Thus, the intragenic duplication is expected to hamper formation of the tetramer, which was suggested to play an important role for long-range chromatin organisation and coordination in gene regulation. (B) Double row of upper incisors in the patient with 32 kb pathogenic duplication within SATB2 at age 3 3/12 years.

Figure 4

Distribution of copy number variants (CNVs) <500 kb in different size ranges and categories. (A) Frequency of pathogenic or likely pathogenic CNVs (pathogenic) versus other CNVs in four size ranges is shown. (B) Frequency of CNV inheritance pattern in five categories: pathogenic or likely pathogenic (pathogenic), likely benign (benign), variants of uncertain significance (VOUS), CNVs with no evidence in favour or against their pathogenicity (no evidence), and incidental findings related to NDDs (incidental). De novo or likely de novo CNVs are indicated as DN, inherited or likely inherited as IN, and homozygous as HO.