ClinVar Genomic variation as it relates to human health

The CLCN1 c.1453A>G (p.Met485Val) missense variant has been reported in at least six studies in which it is found in a total of 13 individuals with myotonia congenita, including two in a homozygous state, ten in a compound heterozygous state (including two siblings) and one proband with unspecified zygosity (Meyer-Kleine et al. 1995; Fialho et al. 2007; Mazon et al. 2012; Skálová et al. 2013; Brugnoni et al. 2013; Hoche et al. 2014). The variant has also been reported in a heterozygous state in at least three unaffected relatives (Meyer-Kleine et al. 1995; Hoche et al. 2014). The p.Met485Val variant was absent from 200 control alleles but is reported at a frequency of 0.000773 in the Other population of the Genome Aggregation Database. Functional studies involving expression in Xenopus oocytes demonstrated that the variant led to a drastic reduction of the single channel conductance compared to wildtype (Wollnik et al. 1997). Based on the evidence, the p.Met485Val variant is classified as pathogenic for myotonia congenita. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.

The frequency of this variant in the general population is consistent with pathogenicity (http://gnomad.broadinstitute.org). This variant has been identified in multiple individuals with recessive myotonia congenita (PMID: 8533761, 18337100, 22094069, 24349310, 24920213). This variant is statistically more frequent in affected individuals than in the general population and/or healthy controls. Assessment of experimental evidence suggests this variant results in abnormal protein function. This variant leads to a reduction in channel conductance (PMID: 9158157). The variant is located in a region that is considered important for protein function and/or structure.

Published functional studies demonstrate variant leads to drastic reduction of single channel conductance, is strongly inwardly rectifying, and incompletely deactivates at negative voltages (Wollnik et al., 1997); This variant is associated with the following publications: (PMID: 23739125, 9736777, 32509969, 33464536, 33314145, 8533761, 25088311, 24920213, 22094069, 9158157, 28427807, 29606556, 17932099, 31544778, 32010054, 31589614)

Variant summary: CLCN1 c.1453A>G (p.Met485Val) results in a conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.0004 in 251490 control chromosomes (gnomAD). c.1453A>G has been reported in the literature as a biallelic genotype in multiple individuals affected with autosomal recessive Congenital Myotonia, including at least one case where it was confirmed to be in trans with a pathogenic variant and was found to segregate with the disease phenotype within members of the same family (e.g. Meyer-Kleine_1995, Suetterlin_2022). These data indicate that the variant is very likely to be associated with disease. At least two publications report experimental evidence evaluating the variant in Xenopus oocytes and found that the variant severely impairs channel function, but does not exert a dominant negative effect when expressed with the wild type protein, consistent with it having an autosomal recessive mode of inheritance (e.g. Wollnik_1997, Suetterlin_2022). The following publications have been ascertained in the context of this evaluation (PMID: 8533761, 34529042, 9158157). Eight submitters have cited clinical-significance assessments for this variant to ClinVar after 2014 with conflicting assessments. The majority of submitters classified the variant as pathogenic (n=6) and others classified it as uncertain significance (n=2). Based on the evidence outlined above, the variant was classified as pathogenic.

This sequence change replaces methionine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 485 of the CLCN1 protein (p.Met485Val). This variant is present in population databases (rs146457619, gnomAD 0.06%). This missense change has been observed in individual(s) with autosomal recessive myotonia congenita (PMID: 8533761, 9736777, 17932099, 18337100, 22094069, 24037712, 24349310). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 280101). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on CLCN1 protein function. Experimental studies have shown that this missense change affects CLCN1 function (PMID: 9158157). For these reasons, this variant has been classified as Pathogenic.

This sequence change in CLCN1 is predicted to replace methionine with valine at codon 485, p.(Met485Val). The methionine residue is highly conserved (100 vertebrates, UCSC), and is a critical methionine residue in the helical transmembrane M-N Linker domain of the chloride ion channel (PMID: 24349310). There is a small physicochemical difference between methionine and valine. The highest population minor allele frequency in the population database gnomAD v2.1 is 0.06% (84/129,188 alleles) in the European (non-Finnish) population. This variant has been detected in multiple individuals with autosomal recessive/Becker myotonia congenita in the homozygous and compound heterozygous state and segregates with recessive disease in at least one family (PMID: 8533761, 24920213, 31544778, 22094069). An in vitro patch-clamp assay with limited validation in Xenopus oocytes demonstrates the variant causes a loss of chloride channel function and no dominant negative effect (PMID: 9158157). Computational evidence predicts a deleterious effect for the missense substitution (REVEL = 0.774). Based on the classification scheme RMH Modified ACMG/AMP Guidelines v1.6.1, this variant is classified as PATHOGENIC. Following criteria are met: PM3_VeryStrong, PM1, PP1, PP3, PS3_Supporting.

The CLCN1 c.1453A>G variant is predicted to result in the amino acid substitution p.Met485Val. This variant has been reported in the homozygous and compound heterozgyous states in mutliple individuals with autosomal recessive myotonia congenita (Dupré et al. 2009. PubMed ID: 18337100; Mazón et al. 2012. PubMed ID: 22094069; Milla et al. 2019. PubMed ID: 31544778; Suetterlin et al. 2022. PubMed ID: 34529042) and has been observed to co-segregate with disease in at least one family (Meyer-Kleine et al. 1995. PubMed ID: 8533761). In vitro functional studies have demonstrated that this variant negatively impacts chloride channel function (Wollnik et al. 1997. PubMed ID: 9158157; Kubisch et al. 1998. PubMed ID: 9736777; Tan et al. 2013. PubMed ID: 24037712; Suetterlin et al. 2022. PubMed ID: 34529042). This variant is reported in 0.065% of alleles in individuals of European (Non-Finnish) descent in gnomAD. Of note, other missense variants at this amino acid residue (p.Met485Lys, p.Met485Glu) have been reported in individuals with CLCN1-related disease (Fialho et al. 2007. PubMed ID: 17932099; Suetterlin et al. 2022. PubMed ID: 34529042). Taken together, this variant is interpreted as pathogenic for autosomal recessive CLCN1-related disorders.

Variant interpreted as Pathogenic and reported on 09-23-2020 by Lab or GTR ID New York Genome Center. Assertions are reported exactly as they appear on the patient provided laboratory report. GenomeConnect does not attempt to reinterpret the variant. The IDDRC-CTSA National Brain Gene Registry (BGR) is a study funded by the U.S. National Center for Advancing Translational Sciences (NCATS) and includes 13 Intellectual and Developmental Disability Research Center (IDDRC) institutions. The study is led by Principal Investigator John Constantino MD PhD from Washington University. The BGR is a data commons of gene variants paired with subject clinical information. This database helps scientists learn more about genetic changes and their impact on the brain and behavior. Participation in the Brain Gene Registry requires participation in GenomeConnect. More information about the Brain Gene Registry can be found on the study website - https://braingeneregistry.wustl.edu/.