Functional and clinical studies reveal pathophysiological complexity of CLCN4-related neurodevelopmental condition

Abstract

Missense and truncating variants in the X-chromosome-linked CLCN4 gene, resulting in reduced or complete loss-of-function (LOF) of the encoded chloride/proton exchanger ClC-4, were recently demonstrated to cause a neurocognitive phenotype in both males and females. Through international clinical matchmaking and interrogation of public variant databases we assembled a database of 90 rare CLCN4 missense variants in 90 families: 41 unique and 18 recurrent variants in 49 families. For 43 families, including 22 males and 33 females, we collated detailed clinical and segregation data. To confirm causality of variants and to obtain insight into disease mechanisms, we investigated the effect on electrophysiological properties of 59 of the variants in Xenopus oocytes using extended voltage and pH ranges. Detailed analyses revealed new pathophysiological mechanisms: 25% (15/59) of variants demonstrated LOF, characterized by a “shift” of the voltage-dependent activation to more positive voltages, and nine variants resulted in a toxic gain-of-function, associated with a disrupted gate allowing inward transport at negative voltages. Functional results were not always in line with in silico pathogenicity scores, highlighting the complexity of pathogenicity assessment for accurate genetic counselling. The complex neurocognitive and psychiatric manifestations of this condition, and hitherto under-recognized impacts on growth, gastrointestinal function, and motor control are discussed. Including published cases, we summarize features in 122 individuals from 67 families with CLCN4-related neurodevelopmental condition and suggest future research directions with the aim of improving the integrated care for individuals with this diagnosis.

Prenatal diagnosis of CLCN4‐related neurodevelopmental disorder in fetuses with congenital brain anomalies

“…Within weeks of this result, personal communication established that this variant had recently been detected in two unrelated individuals presenting postnatally with classic CLCN4 ‐related neurodevelopmental disorder. In one of these individuals, the variant was found to be de novo 2 . The variant found in our family was subsequently re‐classified as likely pathogenic based on its presence in other individuals with consistent features and de novo inheritance (see Table 2 for ACMG/ACGS guidelines criteria).…”

“…In one of these individuals, the variant was found to be de novo. 2 The variant found in our family was subsequently re-classified as likely pathogenic based on its presence in other individuals with consistent features and de novo inheritance (see Table 2 for ACMG/ACGS guidelines criteria).…”

“…Pathogenic CLCN4 variants were first described in 2013 as a cause of early infantile epileptic encephalopathy 3 . Since then, several cohorts have been published in the pediatric literature 2,4–6 . Pathogenic variants in CLCN4 are rare, with only 122 individuals from 67 families currently reported.…”

“…Pathogenic variants in CLCN4 are rare, with only 122 individuals from 67 families currently reported. The molecular and phenotypic spectrum is varied and includes intellectual morbidity, neurodevelopmental delay, seizures, and behavioral and psychiatric disorders 2,4–6 . A prenatal phenotype is not recognised, and the current literature does not mention prenatal scan findings.…”

“…A prenatal phenotype is not recognised, and the current literature does not mention prenatal scan findings. However, non‐specific structural brain malformations have been described postnatally, including hypoplasia of the corpus callosum and ventriculomegaly 2,5,6 …”