rs149729531

chr7-143321432-C-G

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM1 BP4_Strong

The NM_000083.3(CLCN1):c.501C>G(p.Phe167Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000857 in 1,614,204 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

• Frequency:
  • Genomes: 𝑓 0.00079 (1 hom., cov: 33)
  • Exomes 𝑓: 0.00086 (4 hom.)
• Consequence: CLCN1 NM_000083.3 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:6 U:9 B:2 O:2
• Conservation: PhyloP100: 1.72

Genes affected

CLCN1 (HGNC:2019): (chloride voltage-gated channel 1) The CLCN family of voltage-dependent chloride channel genes comprises nine members (CLCN1-7, Ka and Kb) which demonstrate quite diverse functional characteristics while sharing significant sequence homology. The protein encoded by this gene regulates the electric excitability of the skeletal muscle membrane. Mutations in this gene cause two forms of inherited human muscle disorders: recessive generalized myotonia congenita (Becker) and dominant myotonia (Thomsen). Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2012]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM1: In a hotspot region, there are 3 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 7 uncertain in NM_000083.3
• BP4: Computational evidence support a benign effect (MetaRNN=0.0112603605).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CLCN1	NM_000083.3	c.501C>G	p.Phe167Leu	missense_variant	4/23	ENST00000343257.7
CLCN1	NR_046453.2	n.603C>G		non_coding_transcript_exon_variant	4/22

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CLCN1	ENST00000343257.7	c.501C>G	p.Phe167Leu	missense_variant	4/23	1	NM_000083.3	P4

Frequencies

GnomAD3 genomes AF: 0.000795 AC: 121 AN: 152202 Hom.: 1 Cov.: 33

Gnomad AFR AF: 0.0000965

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00105

Gnomad ASJ AF: 0.00778

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000621

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000911

Gnomad OTH AF: 0.00430

GnomAD3 exomes AF: 0.00117 AC: 293 AN: 251484 Hom.: 0 AF XY: 0.00132 AC XY: 179 AN XY: 135916

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00101

Gnomad ASJ exome AF: 0.00833

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.000915

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00116

Gnomad OTH exome AF: 0.00228

GnomAD4 exome AF: 0.000863 AC: 1262 AN: 1461886 Hom.: 4 Cov.: 33 AF XY: 0.000950 AC XY: 691 AN XY: 727240

Gnomad4 AFR exome AF: 0.000538

Gnomad4 AMR exome AF: 0.00123

Gnomad4 ASJ exome AF: 0.00815

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000765

Gnomad4 FIN exome AF: 0.0000562

Gnomad4 NFE exome AF: 0.000691

Gnomad4 OTH exome AF: 0.00176

GnomAD4 genome AF: 0.000794 AC: 121 AN: 152318 Hom.: 1 Cov.: 33 AF XY: 0.000658 AC XY: 49 AN XY: 74482

Gnomad4 AFR AF: 0.0000962

Gnomad4 AMR AF: 0.00105

Gnomad4 ASJ AF: 0.00778

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000621

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000911

Gnomad4 OTH AF: 0.00426

Alfa AF: 0.00177 Hom.: 0

Bravo AF: 0.00100

TwinsUK AF: 0.00135 AC: 5

ALSPAC AF: 0.000519 AC: 2

ESP6500AA AF: 0.000227 AC: 1

ESP6500EA AF: 0.00198 AC: 17

ExAC AF: 0.00109 AC: 132

Asia WGS AF: 0.000289 AC: 1 AN: 3478

EpiCase AF: 0.00207

EpiControl AF: 0.00190

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:6 Uncertain:9 Benign:2 Other:2

Revision: criteria provided, conflicting classifications

Submissions by phenotype

Congenital myotonia, autosomal recessive form Pathogenic:2 Uncertain:3 Other:1

Uncertain significance, criteria provided, single submitter	research	UNC Molecular Genetics Laboratory, University of North Carolina at Chapel Hill	-	The CLCN1 p.Phe167Leu (p.F167L) variant has been reported in several patients with Becker disease (PMID:26510092; 24304580; 17654559; 23739125). However, this variant has also been seen in unaffected individuals (PMID: 27614575). One study reported that the p.F167L variant was associated with more normal function than other deleterious variants and noted that compound heterozygous individuals with p.F167L had a more mild phenotype (PMID: 23933576). -
Uncertain significance, criteria provided, single submitter	clinical testing	Mendelics	May 28, 2019	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Baylor Genetics	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Molecular Genetics, Royal Melbourne Hospital	Mar 01, 2024	This sequence change in CLCN1 is predicted to replace phenylalanine with leucine at codon 167, p.(Phe167Leu). The phenylalanine residue is moderately conserved (100 vertebrates, Multiz Alignments), and is located in the transmembrane alpha-helix C domain (PMID: 23739125, 34529042). There is a small physicochemical difference between phenylalanine and leucine. The highest population minor allele frequency in the population database gnomAD v4.0 is 0.1% (71/60,026 alleles, 1 homozygote) in the Admixed American population. This variant has been detected in the homozygous and compound heterozygous state (with at least one individual confirmed in trans with a pathogenic variant) in multiple individuals with autosomal recessive myotonia congenita (ARMC) (PMID: 22094069, 23739125, 28427807, 31544778, 33263785, 33573884, 34529042). The variant has been reported to segregate with ARMC in at least two families (PMID: 21221019). There are inconsistent reports of this variant heterozygous in association with autosomal dominant myotonia congenita (PMID: 21387378, 26510092, 27614575). This variant is also commonly reported in cis with c.313C>T p.(Arg105Cys) in individuals with ARMC (PMID: 21221019, 21387378, 22094069, 22109722, 23739125, 24349310, 28427807, 31544778, 33573884). Patch clamp assays measuring voltage-dependent activation in Xenopus oocytes and mammalian cell lines are conflicting from no obvious differences in chloride channel voltage to a modest positive shift in the voltage dependence of activation (PMID: 10690989, 23933576, 26510092, 34529042). The assay demonstrating a modest positive shift suggests the variant behaves similarly to ARMC variants without dominant-negative effects (PMID: 34529042). Computational evidence is uninformative for the missense substitution (REVEL = 576). 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, PP1_Moderate. -
Affects, no assertion criteria provided	clinical testing	Laboratory of Medical Genetics, National & Kapodistrian University of Athens	Feb 20, 2024	Advanced modeling of protein structural, functional, and spatial characteristics, amino acid conservations physicochemical variations, residues mobility, and thermodynamic stability details emerging from several studies indicate that the c.501C>G missense variant behaves similarly to the wild-type, with little or no evidence supportive of a deleterious effect for the CLCN1 channel. In consistence with the findings of the current cohort it could be suggested that c.501C>G, p.(Phe167Leu) is most probably acting as a modifier of the severity of symptoms if and when affected phenotypes are generated from co-existing pathogenic variants. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Centre for Mendelian Genomics, University Medical Centre Ljubljana	Jan 01, 2016	This variant was classified as: Likely pathogenic. -

not provided Pathogenic:1 Uncertain:4

Uncertain significance, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Mar 01, 2022	CLCN1: PM3, PM2:Supporting -
Uncertain significance, criteria provided, single submitter	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	Mar 29, 2023	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Jul 21, 2022	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center	Aug 07, 2022	BP4 -
Pathogenic, criteria provided, single submitter	clinical testing	Athena Diagnostics	Aug 04, 2021	This variant is statistically more frequent in affected individuals than in the general population and/or healthy controls. Therefore, the frequency of this variant in the general population is consistent with pathogenicity (Genome Aggregation Database (gnomAD), Cambridge, MA (URL: http://gnomad.broadinstitute.org)). This variant has been reported in multiple families with autosomal recessive myotonia congenita (PMID: 18337730, 21221019, 24037712, 23739125). Although there are heterozygous carriers with disease, this variant has also been reported in asymptomatic individuals (PMID: 17932099, 21698652, 26510092, 7874130, 27614575). Therefore, the data only supports a recessive association with CLCN1-related conditions. In multiple individuals, this variant has been seen with a single recessive pathogenic variant in the same gene, suggesting this variant may also be pathogenic. -

not specified Uncertain:1 Benign:1

Uncertain significance, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Jan 15, 2024	Variant summary: CLCN1 c.501C>G (p.Phe167Leu) results in a non-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 0.00086 in 1614204 control chromosomes in the gnomAD database, including 5 homozygotes. This frequency is not significantly higher than estimated for a pathogenic variant in CLCN1 causing Myotonia congenita (0.00086 vs 0.0035), allowing no conclusion about variant significance. c.501C>G has been reported in the literature at a compound heterozygous state in individuals affected with autosomal recessive Myotonia congenita (examples, Gorukmez_2023, Bozovic_2021, Suetterlin_2022, Vereb_2020). It has also been reported at a heterozygous in several individuals with autosomal dominant Myotonia congenita and often along with a pathogenic variant from another gene that may fully explain the phenotype (example, Peddareddygari_2016, Maggi_2017). These report(s) do not provide unequivocal conclusions about association of the variant with Myotonia congenita. Several publications report experimental evidence evaluating an impact on protein function. These results showed no damaging or marginal effect of this variant on the electrophysiological metrics of CLCN1 by whole-cell patch clamping in HEK293T cells or in xenopus oocytes (Desaphy_2013, Zhang_2000, Suetterlin_2022). The following publications have been ascertained in the context of this evaluation (PMID: 34106991, 23933576, 28993909, 27266866, 34529042, 10690989, 36964972). ClinVar contains an entry for this variant (Variation ID: 209138). Based on the evidence outlined above, the variant was classified as uncertain significance. -
Likely benign, criteria provided, single submitter	clinical testing	GeneDx	Dec 28, 2017	This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Congenital myotonia, autosomal recessive form;C2936781:Congenital myotonia, autosomal dominant form Uncertain:1 Other:1

not provided, no classification provided	phenotyping only	GenomeConnect - Invitae Patient Insights Network	-	Variant interpreted as Uncertain significance and reported on 07-16-2020 by Invitae. GenomeConnect-Invitae Patient Insights Network assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. Registry team members make no attempt to reinterpret the clinical significance of the variant. Phenotypic details are available under supporting information. -
Uncertain significance, criteria provided, single submitter	clinical testing	Invitae	Nov 01, 2022	This sequence change replaces phenylalanine, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 167 of the CLCN1 protein (p.Phe167Leu). This variant is present in population databases (rs149729531, gnomAD 0.8%), and has an allele count higher than expected for a pathogenic variant. This missense change has been observed in individual(s) with autosomal recessive myotonia congenita (Becker disease), and often co-occurs (likely on the same chromosome) with p.Arg105Cys (PMID: 17654559, 18337730, 21221019, 22094069, 22521272, 22641783, 23113340, 23739125, 24037712, 24304580, 24349310, 24452722, 27199537). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 209138). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. Experimental studies are conflicting or provide insufficient evidence to determine the effect of this variant on CLCN1 function (PMID: 10690989, 23933576, 24304580, 26510092). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -

Tip-toe gait Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Practice for Gait Abnormalities, David Pomarino, Competency Network Toe Walking c/o Practice Pomarino

Jun 25, 2021

The variant causes the exchange of phenylanaline by leucine at position 167 of the CLCN1 protein and is located in one of the transmembrane helical motifs that play a role in the ion selectivity of the chloride channel. -

Congenital myotonia, autosomal dominant form Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Baylor Genetics

Jul 09, 2015

This variant has been previously reported as disease-causing in a recessive state, so heterozygotes would be carriers. -

Myotonia Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Centre for Mendelian Genomics, University Medical Centre Ljubljana

Jan 23, 2015

- -

Batten-Turner congenital myopathy Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Mar 06, 2018

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.84
BayesDel_addAF	Benign	-0.11	T
BayesDel_noAF	Uncertain	0.030
Cadd	Benign	22
Dann	Benign	0.97
Eigen	Benign	-0.29
Eigen_PC	Benign	-0.13
FATHMM_MKL	Uncertain	0.83	D
LIST_S2	Uncertain	0.92	D;D
M_CAP	Uncertain	0.11	D
MetaRNN	Benign	0.011	T;T
MetaSVM	Benign	-0.31	T
MutationTaster	Benign	0.95	D
PrimateAI	Uncertain	0.62	T
Polyphen		0.21	.;B
Vest4		0.82
MutPred		0.76		Gain of catalytic residue at T166 (P = 0.4228);Gain of catalytic residue at T166 (P = 0.4228);
MVP		0.92
MPC		0.31
ClinPred		0.032	T
GERP RS		4.1
Varity_R		0.49
gMVP		0.69

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs149729531; hg19: chr7-143018525;