A novel homozygous KCNQ3 loss‐of‐function variant causes non‐syndromic intellectual disability and neonatal‐onset pharmacodependent epilepsy

Abstract

Objective Heterozygous variants in KCNQ2 or, more rarely, KCNQ3 genes are responsible for early‐onset developmental/epileptic disorders characterized by heterogeneous clinical presentation and course, genetic transmission, and prognosis. While familial forms mostly include benign epilepsies with seizures starting in the neonatal or early‐infantile period, de novo variants in KCNQ2 or KCNQ3 have been described in sporadic cases of early‐onset encephalopathy (EOEE) with pharmacoresistant seizures, various age‐related pathological EEG patterns, and moderate/severe developmental impairment. All pathogenic variants in KCNQ2 or KCNQ3 occur in heterozygosity. The aim of this work was to report the clinical, molecular, and functional properties of a new KCNQ3 variant found in homozygous configuration in a 9‐year‐old girl with pharmacodependent neonatal‐onset epilepsy and non‐syndromic intellectual disability. Methods Exome sequencing was used for genetic investigation. KCNQ3 transcript and subunit expression in fibroblasts was analyzed with quantitative real‐time PCR and Western blotting or immunofluorescence, respectively. Whole‐cell patch‐clamp electrophysiology was used for functional characterization of mutant subunits. Results A novel single‐base duplication in exon 12 of KCNQ3 (NM_004519.3:c.1599dup) was found in homozygous configuration in the proband born to consanguineous healthy parents; this frameshift variant introduced a premature termination codon (PTC), thus deleting a large part of the C‐terminal region. Mutant KCNQ3 transcript and protein abundance was markedly reduced in primary fibroblasts from the proband, consistent with nonsense‐mediated mRNA decay. The variant fully abolished the ability of KCNQ3 subunits to assemble into functional homomeric or heteromeric channels with KCNQ2 subunits. Significance The present results indicate that a homozygous KCNQ3 loss‐of‐function variant is responsible for a severe phenotype characterized by neonatal‐onset pharmacodependent seizures, with developmental delay and intellectual disability. They also reveal difference in genetic and pathogenetic mechanisms between KCNQ2 ‐ and KCNQ3 ‐related epilepsies, a crucial observation for patients affected with EOEE and/or developmental disabilities.

Heteromeric Kv7.2 current changes caused by loss-of-function of KCNQ2 mutations are correlated with long-term neurodevelopmental outcomes

“…When recorded the HEK293 cells without transfected KCNQ2, the currents closely resembled those for homomeric S247X, which indicated that homomeric S247X was not functional in the present study. That is compatible with S247X by nonsense-mediated mRNA decay [46][47][48] and removing all C-terminal domain for tetramerisation of functional channels, is supposed to be nonfunctional. HEK 293 cells have been widely used in cell biology and the gene expression in HEK 293 cells is like that of the neuron.…”

“…The hypothesis is verified in clinical phenotypes for which seizures improved after the age of 1 month. We predict that the S247X nonsense mutation caused a lower expression of the KCNQ2 protein due to nonsense-mediated mRNA decay [46][47][48] , which activated hetero-KCNQ2 and KCNQ3 functional compensation. However, a decrease in the expression of the KCNQ2 protein in S247L and S247W was not predicted.…”

The Role of Kv7.2 in Neurodevelopment: Insights and Gaps in Our Understanding

“…The incidence of KCNQ2-E is reported to be 1-3/100.000 births (Lopez-Rivera et al, 2020). By contrast, only a handful of DEE patients with pathogenic variants in KCNQ3 or KCNQ5 have been described (Rauch et al, 2012;Epi4k Consortium et al, 2013;Lehman et al, 2017;Ambrosino et al, 2018;Kothur et al, 2018;Lauritano et al, 2019;Rosti et al, 2019;Sands et al, 2019).…”

“…During the last decade, an emerging number of studies pointed out that severe disruption of the function of Kv7.2, Kv7.3, and Kv7.5 subunits due to de pathogenic variants in the encoding gene leads to developmental and epileptic encephalopathy (DEE;Weckhuysen et al, 2012;Lehman et al, 2017;Lauritano et al, 2019). DEEs are a heterogeneous group of mostly neonatal-, infantile-or childhood-onset disorders characterized by severe, drug-resistant seizures, characteristic electroencephalographic (EEG) signatures, and different levels of developmental delay or regression, often with a poor prognosis.…”

A Novel Kv7.3 Variant in the Voltage-Sensing S4 Segment in a Family With Benign Neonatal Epilepsy: Functional Characterization and in vitro Rescue by β-Hydroxybutyrate

“…Several pieces of evidence support this view; as an example, while heterozygous frameshift variants in KCNQ2 are frequent causes of BFNE (Miceli et al, 2018), no heterozygous pathogenic frameshift KCNQ3 variant has ever been associated with a human phenotype. In addition, no individual carrying KCNQ2 frameshift variants in homozygosity has ever been described, as minimal KCNQ2 residual activity is probably essential for survival (Lauritano et al, 2019); by contrast, two recent studies reported the occurrence of homozygous frameshift variants in KCNQ3 (each inherited from an asymptomatic parent) in patients with developmental delay and neonatal seizures (Kothur et al, 2018;Lauritano et al, 2019), demonstrating that, homozygous variants in KCNQ3 are compatible with life. Moreover, a distinct functional role of these two genes emerging from developmental and genetic studies in humans, appears also to be recapitulated in mice.…”