Translating genetic and functional data into clinical practice: a series of 223 families with myotonia

Abstract

High throughput DNA sequencing is increasingly employed to diagnose single gene neurological and neuromuscular disorders. Large volumes of data present new challenges in data interpretation and its useful translation into clinical and genetic counselling for families. Even when a plausible gene is identified with confidence, interpretation of the clinical significance and inheritance pattern of variants can be challenging. We report our approach to evaluating variants in the skeletal muscle chloride channel ClC-1 identified in 223 probands with myotonia congenita (MC) as an example of these challenges. Sequencing of CLCN1, the gene that encodes CLC-1, is central to the diagnosis of MC. However, interpreting the pathogenicity and inheritance pattern of novel variants is notoriously difficult as both dominant and recessive mutations are reported throughout the channel sequence, ClC-1 structure-function is poorly understood and significant intra- and interfamilial variability in phenotype is reported. Heterologous expression systems to study functional consequences of CIC-1 variants are widely reported to aid the assessment of pathogenicity and inheritance pattern. However, heterogeneity of reported analyses does not allow for the systematic correlation of available functional and genetic data. We report the systematic evaluation of 95 CIC-1 variants in 223 probands, the largest reported patient cohort, in which we apply standardised functional analyses and correlate this with clinical assessment and inheritance pattern. Such correlation is important to determine if functional data improves the accuracy of variant interpretation and likely mode of inheritance. Our data provide an evidence-based approach that functional characterisation of ClC-1 variants improves clinical interpretation of their pathogenicity and inheritance pattern and serve as reference for 34 previously unreported and 28 previously uncharacterised CLCN1 variants. In addition, we identify novel pathogenic mechanisms and find that variants that alter voltage dependence of activation cluster in the first half of the transmembrane domains and variants that yield no currents cluster in the second half of the transmembrane domain. None of the variants in the intracellular domains were associated with dominant functional features or dominant inheritance pattern of MC. Our data help provide an initial estimate of the anticipated inheritance pattern based on the location of a novel variant and shows that systematic functional characterisation can significantly refine the assessment of risk of an associated inheritance pattern and consequently the clinical and genetic counselling.

A novel mutation of the CLCN1 gene in a cat with myotonia congenita: Diagnosis and treatment

“…The ClC‐1 protein is a homodimer formed from both alleles, and in dominant forms of the disease the variant allele can produce a mutant subunit that exhibits a dominant‐negative effect on the wild‐type subunit of the channel, usually by alteration of the voltage dependence of the channel. Recessive forms tend to be protein truncations as found in our cat and in the previously reported cases in cats 25 . In our case, only the first 3 exons of the 23‐exon gene could be translated, causing a markedly altered protein structure which in turn resulted in prominent clinical signs of myotonia.…”

“…Recessive forms tend to be protein truncations as found in our cat and in the previously reported cases in cats. 25 In our case, only the first 3 exons of the 23‐exon gene could be translated, causing a markedly altered protein structure which in turn resulted in prominent clinical signs of myotonia. However, the clinical signs in our cat were consistent with those previously reported in cats with a variant in exon 16.…”

“… 23 , 24 Myotonia congenita can be inherited as an autosomal dominant or recessive trait, with dominant forms causing more severe signs in people, but the genotype‐phenotype correlation is complicated and somewhat difficult to predict. 25 The ClC‐1 protein is a homodimer formed from both alleles, and in dominant forms of the disease the variant allele can produce a mutant subunit that exhibits a dominant‐negative effect on the wild‐type subunit of the channel, usually by alteration of the voltage dependence of the channel. Recessive forms tend to be protein truncations as found in our cat and in the previously reported cases in cats.…”

“…Therefore, chloride channelopathies decrease chloride ion conductance, and if net chloride conductance is <50% of normal, clinical signs occur 23,24 . Myotonia congenita can be inherited as an autosomal dominant or recessive trait, with dominant forms causing more severe signs in people, but the genotype‐phenotype correlation is complicated and somewhat difficult to predict 25 . The ClC‐1 protein is a homodimer formed from both alleles, and in dominant forms of the disease the variant allele can produce a mutant subunit that exhibits a dominant‐negative effect on the wild‐type subunit of the channel, usually by alteration of the voltage dependence of the channel.…”

The spectrum of hereditary neuromuscular disorders in the Pakistani population

“…Another variant at the same amino acid position, has been reported but classified as a VUS (ClinVar ID: 1190052) (ClinVar, 2022). The variant in within the transmembrane domain and is likely to impact the CLCN1 function and correlate with the autosomal recessive myotonia by reducing the functional expression of the channel, that was studied by Suetterlin et al (Khadilkar et al, 2017) Furthermore, missense variants in CLCN1 are known to be disease‐causing in nature (Liu et al, 2015; Suetterlin et al, 2022). With these lines of evidence, we reclassify this variant from VUS to Likely Pathogenic, based on ACMG scoring (PM1, PP2, PP3, PP4, and PP5).…”