NM_000083.3(CLCN1):c.1606G>A (p.Val536Ile) AND Congenital myotonia, autosomal recessive form

Germline classification:: Likely pathogenic (1 submission)
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV003338626.2

Allele description [Variation Report for NM_000083.3(CLCN1):c.1606G>A (p.Val536Ile)]

NM_000083.3(CLCN1):c.1606G>A (p.Val536Ile)

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.1606G>A (p.Val536Ile)

HGVS:

NC_000007.14:g.143341952G>A
NG_009815.2:g.30827G>A
NM_000083.3:c.1606G>AMANE SELECT
NP_000074.3:p.Val536Ile
NC_000007.13:g.143039045G>A
NG_009815.1:g.30827G>A
NM_000083.2:c.1606G>A
NR_046453.2:n.1561G>A

Protein change:

V536I

Links:

dbSNP: rs777685454

NCBI 1000 Genomes Browser:

rs777685454

Molecular consequence:

NM_000083.3:c.1606G>A - missense variant - [Sequence Ontology: SO:0001583]
NR_046453.2:n.1561G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Congenital myotonia, autosomal recessive form
Synonyms:: Myotonia congenita autosomal recessive; Becker disease; Myotonia generalized; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0009715; MedGen: C0751360; Orphanet: 614; OMIM: 255700

Recent activity

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Homo sapiens matrix remodeling associated 8 (MXRA8), transcript variant 4, mRNA
Homo sapiens matrix remodeling associated 8 (MXRA8), transcript variant 4, mRNA
gi|1677530683|ref|NM_001282583.2|

Nucleotide
Homo sapiens matrix remodeling associated 8 (MXRA8), transcript variant 3, mRNA
Homo sapiens matrix remodeling associated 8 (MXRA8), transcript variant 3, mRNA
gi|1890259879|ref|NM_001282584.2|

Nucleotide
cadherin EGF LAG seven-pass G-type receptor 3 precursor [Rattus norvegicus]
cadherin EGF LAG seven-pass G-type receptor 3 precursor [Rattus norvegicus]
gi|13786140|ref|NP_112610.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004047996	Neuberg Centre For Genomic Medicine, NCGM	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004047996

Neuberg Centre For Genomic Medicine, NCGM

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Neuberg Centre For Genomic Medicine, NCGM, SCV004047996.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

The CLCN1 c.1606G>A (p.Val536Ile) variant has been observed in individuals with autosomal recessive myotonia congenita and late onset myotonia (Raheem O et al, Ferese R et al). This p.Val536Ile variant has allele frequency of 0.002829% in the gnomAD and novel (not in any individuals) in 1000 genome database. It has been submitted to ClinVar with varying interpretations: Pathogenic/ Likely Pathogenic. The amino acid Val at position 536 is changed to a Ile changing protein sequence and it might alter its composition and physico-chemical properties. The amino acid change p.Val536Ile in CLCN1 is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. For these reasons, this variant has been classified as Likely Pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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