Submission Details

CLCN6 was first reported in relation to autosomal dominant condition, “neurodegeneration, childhood-onset, hypotonia, respiratory insufficiency and brain imaging abnormalities” in 2020 (Polovitskaya et al., PMID: 33217309). This gene encodes a Cl- /H+ antiporter primarily expressed in neuronal cells and localizes to late endosome-lysosome compartments (PMID: 16950870, 33708769, 17534424). The voltage-dependent Cl- /H+ exchanger activity of CLCN6 is pH-dependent and relies on a V-ATPase pump to maintain acidic homeostasis within these compartments (PMID: 20466723, 37831762). At least three unique missense variants have been identified in five unrelated individuals across three publications (PMID: 33217309, 37831762; 33590434). Affected individuals presented severe global developmental delays, regression, generalized hypotonia, abnormal brain imaging, respiratory insufficiency, vision impairment, and feeding difficulties. Additional features include seizures, neurogenic bladder, short stature, microcephaly, temperature dysregulation, skin anomalies, neuropathy, and variable craniofacial dysmorphism. Notably, among these variants, the de novo CLCN6 c.1658A>G, p.(Tyr553Cys) variant is shared by three of the five affected individuals, while the remaining two patients carry de novo c.1558A>G, p.(Thr520Ala) and c.599A>C, p.(Glu200Ala) variants, respectively. The reported pathogenic mechanism involves a gain of function. Electrophysiological analyses demonstrated that both the p.Tyr553Cys and p.Thr520Ala variants induce larger, steady currents by selectively transporting Cl- independently of the acidic environment, using energy provided by ATP pumps at lower voltages compared to the wild type (PMID: 33217309, 37831762). Overexpression of these variants in Hela cells leads to the formation of giant cytoplasmic vacuoles resulting from the fusion of multiple small vesicles over time. These vacuoles exhibit reduced acidity, impaired endocytosis, and lysosomal enzyme incorporation (PMID: 33217309, 37831762). Structural modeling suggests that the p.Tyr553Cys and p.Thr520Ala variants form a mutation hotspot within an interaction network (PMID: 37831762). Furthermore, experimental evidence indicates that other variants at the same codon 553 may have a similar impact (PMID: 37831762). The experimental assays on the c.599A>C, p.(Glu200Ala) variant demonstrated similar disruption of the lysosomal system. Heterologous expression of this variant in Xenopus does not alter CLCN6 localization but blocks proton transposition, resulting in a change in Cl-/H+ exchanger activity (PMID: 20466723). In the presence of this CLCN6 variant, cytoplasmic vesicles are mildly enlarged and fail to incorporate lysosomal enzymes. Additionally, the mutant increases autophagosome accumulation by inhibiting autophagosome degradation and fusion with the lysosome (PMID: 33590434). These results suggested the impact of CLCN6 protein in the late endo-lysosomal pathway on the neurodegenerative disease. In summary, there is moderate evidence supporting the relationship between CLCN6 and “neurodegeneration, childhood-onset, hypotonia, respiratory insufficiency and brain imaging abnormalities”. Of note, this classification only focuses on gain-of-function mechanisms while loss-of-function mechanisms reportedly associated with mild neuronal ceroid lipofuscinosis in mice model (PMID: 16950870) and frontotemporal dementia (PMID: 33737586) were not curated in this entry. This classification was approved by the ClinGen Lysosomal Diseases GCEP on May 7, 2024 (SOP Version 10).