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NM_000083.3(CLCN1):c.2680C>T (p.Arg894Ter) AND Congenital myotonia, autosomal dominant form

Germline classification:
Pathogenic (5 submissions)
Last evaluated:
Sep 26, 2023
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV000019099.40

Allele description [Variation Report for NM_000083.3(CLCN1):c.2680C>T (p.Arg894Ter)]

NM_000083.3(CLCN1):c.2680C>T (p.Arg894Ter)

Gene:
CLCN1:chloride voltage-gated channel 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
7q34
Genomic location:
Preferred name:
NM_000083.3(CLCN1):c.2680C>T (p.Arg894Ter)
HGVS:
  • NC_000007.14:g.143351678C>T
  • NG_009815.2:g.40553C>T
  • NM_000083.3:c.2680C>TMANE SELECT
  • NP_000074.3:p.Arg894Ter
  • NC_000007.13:g.143048771C>T
  • NG_009815.1:g.40553C>T
  • NM_000083.2:c.2680C>T
  • NR_046453.2:n.2635C>T
  • p.Arg894*
  • p.Arg894X
Protein change:
R894*; ARG894TER
Links:
OMIM: 118425.0015; dbSNP: rs55960271
NCBI 1000 Genomes Browser:
rs55960271
Molecular consequence:
  • NR_046453.2:n.2635C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_000083.3:c.2680C>T - nonsense - [Sequence Ontology: SO:0001587]
Observations:
1

Condition(s)

Name:
Congenital myotonia, autosomal dominant form (THD)
Synonyms:
Myotonia congenita autosomal dominant; Thomsen disease; Thomsen's disease
Identifiers:
MONDO: MONDO:0008055; MedGen: C2936781; Orphanet: 614; OMIM: 160800

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000039387OMIM
no assertion criteria provided
Pathogenic
(May 1, 2009)
germlineliterature only

PubMed (4)
[See all records that cite these PMIDs]

SCV000966882Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
criteria provided, single submitter

(LMM Criteria)
Pathogenic
(Aug 9, 2018)
germlineclinical testing

PubMed (11)
[See all records that cite these PMIDs]

SCV001428781Institute of Human Genetics, University of Leipzig Medical Center
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Sep 26, 2023)
unknownclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV002518713Mendelics
criteria provided, single submitter

(Mendelics Assertion Criteria 2019)
Pathogenic
(May 4, 2022)
germlineclinical testing

Citation Link,

SCV002579211MGZ Medical Genetics Center
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Jul 28, 2022)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes12not providednot providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedunknownyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlinenot provided11not providednot providednot providedliterature only, clinical testing

Citations

PubMed

Myotonia caused by mutations in the muscle chloride channel gene CLCN1.

Pusch M.

Hum Mutat. 2002 Apr;19(4):423-34. Review.

PubMed [citation]
PMID:
11933197

Clinical, electrophysiologic, and genetic study of non-dystrophic myotonia in French-Canadians.

Dupré N, Chrestian N, Bouchard JP, Rossignol E, Brunet D, Sternberg D, Brais B, Mathieu J, Puymirat J.

Neuromuscul Disord. 2009 May;19(5):330-4. doi: 10.1016/j.nmd.2008.01.007. Epub 2008 Mar 11.

PubMed [citation]
PMID:
18337100
See all PubMed Citations (14)

Details of each submission

From OMIM, SCV000039387.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (4)

Description

For discussion of the arg894-to-ter (R894X) mutation in the CLCN1 gene that was found in compound heterozygous state in sibs with autosomal recessive myotonia congenita (255700) by Pusch et al. (1995), see 118425.0010.

In patients with both autosomal recessive and autosomal dominant (160800) myotonia congenita, Meyer-Kleine et al. (1995) identified a mutation in the CLCN1 gene, resulting in an R894X substitution. Functional expression of the R894X mutant in Xenopus oocytes revealed a large reduction, but not complete abolition, of chloride currents. Further, it had a weak dominant-negative effect on wildtype currents in coexpression studies. Reduction of currents predicted for heterozygous carriers were close to the borderline value, sufficient to elicit myotonia.

Sun et al. (2001) found a carrier frequency of 0.87% for the R894X mutation in the northern Scandinavian population.

In a French Canadian family with myotonia, Dupre et al. (2009) found that the R894X mutation could be expressed in a semidominant or recessive manner. The proband, who was heterozygous for the R894X mutation, had muscle stiffness and mild warm-up phenomenon, but no significant percussion myotonia and no myotonia on EMG. In contrast, her daughters, who were compound heterozygous for the R894X and R300X (118425.0017) mutations, showed a moderately severe phenotype with generalized hypertrophy consistent with autosomal recessive Becker myotonia. This compound heterozygous genotype showed resistance to phenytoin, mexiletine, and quinine.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot providednot providednot providednot provided

From Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV000966882.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (11)

Description

The p.Arg894X variant in CLCN1 has been reported in >25 homozygous and compound heterozygous individuals with clinical features of myotonia congenita and segreg ated with disease in many affected relatives (Brugnoni 2013, Fialho 2007, Mazon 2012, Meyer-Kleine 1995, Neroldova 2016, Sun 2001, Tincheva 2016, Trip 2008, Zie lonka 2012). It is a common pathogenic variant in Scandinavian populations, wher e the disease prevalence is approximately 1 in 10,000 versus 1 in 100,000 worldw ide (Sun 2001). This variant has been identified in 1.63% (429/25792) of Finnish chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinst itute.org) and reported in ClinVar (Variation ID# 17545). This nonsense variant leads to a premature termination codon at position 894. This alteration occurs w ithin the last exon and is more likely to escape nonsense mediated decay (NMD) a nd result in a truncated protein. In vitro functional studies provide some evide nce that the p.Arg894X variant impacts protein function (Meyer-Kleine 1995). In summary, this variant meets criteria to be classified as pathogenic for myotonia congenita in an autosomal recessive manner based upon segregation studies, func tional evidence and predicted impact on protein. ACMG/AMP Criteria applied: PM3_ VeryStrong, PP1_Strong, PS3_Moderate.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot provided1not provided1not provided

From Institute of Human Genetics, University of Leipzig Medical Center, SCV001428781.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

Criteria applied: PM3_VSTR,PVS1_MOD,PS3_MOD

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot providednot providednot providednot providednot provided

From Mendelics, SCV002518713.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From MGZ Medical Genetics Center, SCV002579211.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided12not providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided12not providednot providednot provided

Last Updated: Oct 20, 2024