Neurodevelopmental Disorders in Patients With Complex Phenotypes and Potential Complex Genetic Basis Involving Non-Coding Genes, and Double CNVs

Abstract

Neurodevelopmental disorders (NDDs) are a heterogeneous class of brain diseases, with a complex genetic basis estimated to account for up to 50% of cases. Nevertheless, genetic diagnostic yield is about 20%. Array-comparative genomic hybridization (array-CGH) is an established first-level diagnostic test able to detect pathogenic copy number variants (CNVs), however, most identified variants remain of uncertain significance (VUS). Failure of interpretation of VUSs may depend on various factors, including complexity of clinical phenotypes and inconsistency of genotype-phenotype correlations. Indeed, although most NDD-associated CNVs are de novo, transmission from unaffected parents to affected children of CNVs with high risk for NDDs has been observed. Moreover, variability of genetic components overlapped by CNVs, such as long non-coding genes, genomic regions with long-range effects, and additive effects of multiple CNVs can make CNV interpretation challenging. We report on 12 patients with complex phenotypes possibly explained by complex genetic mechanisms, including involvement of antisense genes and boundaries of topologically associating domains. Eight among the 12 patients carried two CNVs, either de novo or inherited, respectively, by each of their healthy parents, that could additively contribute to the patients’ phenotype. CNVs overlapped either known NDD-associated or novel candidate genes (PTPRD, BUD13, GLRA3, MIR4465, ABHD4, and WSCD2). Bioinformatic enrichment analyses showed that genes overlapped by the co-occurring CNVs have synergistic roles in biological processes fundamental in neurodevelopment. Double CNVs could concur in producing deleterious effects, according to a two-hit model, thus explaining the patients’ phenotypes and the incomplete penetrance, and variable expressivity, associated with the single variants. Overall, our findings could contribute to the knowledge on clinical and genetic diagnosis of complex forms of NDD.

Family-Based Whole-Exome Analysis of Specific Language Impairment (SLI) Identifies Rare Variants in BUD13, a Component of the Retention and Splicing (RES) Complex

“…Transcriptomic analysis of RES complex genes in the mutant zebrafish identified the features of RES dependent introns [ 79 ]. Although no rare variants in BUD13 are reportedly causative in other genetic disorders, a copy number variant (CNV) investigation revealed a deletion in chromosome 11 spanning BUD13 in an individual with an NDD phenotype [ 80 ]. The same individual showed a deletion in chromosome 9 encompassing PTPRD , suggesting an additive effect in this patient [ 80 ].…”

“…Although no rare variants in BUD13 are reportedly causative in other genetic disorders, a copy number variant (CNV) investigation revealed a deletion in chromosome 11 spanning BUD13 in an individual with an NDD phenotype [ 80 ]. The same individual showed a deletion in chromosome 9 encompassing PTPRD , suggesting an additive effect in this patient [ 80 ]. Additionally, the risk of developing a metabolic syndrome was associated with BUD13 through case-control studies [ 81 , 82 ].…”

“…Regulation of mRNAs through splicing and other mechanisms like non-coding RNAs are proposed in LI and other NDDs [ 66 , 86 , 87 ]. The CNVs spanning BUD13 and PTPRD identified in a patient with NDD suggest a multiple hit model and signifies a role of the RES complex in brain associated phenotypes in humans [ 80 ]. We suggest BUD13 regulates the expression of other neuronal genes through splicing and IR for the development of language abilities.…”

“…Subsequently, the Sanger sequencing of these genes in other unrelated individuals with SLI identified additional genetic variants, some observed in multiple proband-ascertained families. We prioritized BUD13 among other candidates based on the high frequency of individuals with SLI carrying genetic variants in this gene and its role in the mechanisms thought to be involved in neural phenotypes [ 79 , 80 , 90 , 91 , 92 ]. Genetic study of BUD13 in SLI samples from other populations may provide more information about the genotype—phenotype relationship.…”

Incomplete Penetrance and Variable Expressivity: From Clinical Studies to Population Cohorts

“…Significant allelic imbalance has been observed in up to 88% of genes in human tissues, potentially caused by genetic modifiers or stochastic factors ( Aguet et al, 2017 ), and has been identified as both tissue-specific and genome-wide in mouse models ( Pinter et al, 2015 ). Structural variants such as duplications that are in trans with a pathogenic LoF variant can alleviate the potential clinical phenotype when disease would be caused by haploinsufficiency, by providing an additional WT copy of a gene, thus resulting in a normal level of gene expression ( Servetti et al, 2021 ), as has been observed in DiGeorge syndrome ( Carelle-Calmels et al, 2009 ). Additional variants in the untranslated regions of mRNA can also affect the translational efficiency and gene expression can also vary widely across tissues, highlighting the importance of sequencing disease-relevant tissue in the interpretation of genetic variation ( Cummings et al, 2017 ; Mignone et al, 2002 ).…”