NM_000083.3(CLCN1):c.568G>A (p.Gly190Arg) AND not provided

This record was updated by the submitter. Please see the current version.

Germline classification:: Conflicting interpretations of pathogenicity (5 submissions)
Last evaluated:: Apr 20, 2021
Review status:: criteria provided, conflicting classifications

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:: RCV000711236.34

Allele description

NM_000083.3(CLCN1):c.568G>A (p.Gly190Arg)

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.568G>A (p.Gly190Arg)

HGVS:

NC_000007.14:g.143321720G>A
NG_009815.2:g.10595G>A
NM_000083.3:c.568G>AMANE SELECT
NP_000074.3:p.Gly190Arg
NC_000007.13:g.143018813G>A
NG_009815.1:g.10595G>A
NM_000083.2:c.568G>A
NR_046453.2:n.670G>A

Protein change:

G190R

Links:

dbSNP: rs369773321

NCBI 1000 Genomes Browser:

rs369773321

Molecular consequence:

NM_000083.3:c.568G>A - missense variant - [Sequence Ontology: SO:0001583]
NR_046453.2:n.670G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Homo sapiens oxysterol binding protein like 6 (OSBPL6), transcript variant 3, mR...
Homo sapiens oxysterol binding protein like 6 (OSBPL6), transcript variant 3, mRNA
gi|319996734|ref|NM_001201480.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000343271	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL Classification Definitions 2015)	Uncertain significance (Jun 27, 2016)	germline	clinical testing	Citation Link,
SCV000841568	Athena Diagnostics	criteria provided, single submitter (Athena Diagnostics Criteria)	Likely pathogenic (Sep 23, 2019)	unknown	clinical testing	PubMed (6) [See all records that cite these PMIDs] 29606556, 23810313, 24349310, 22987687, 24037712, 26467025
SCV001248202	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Pathogenic (Apr 1, 2019)	germline	clinical testing	Citation Link,
SCV001822902	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Likely pathogenic (Apr 20, 2021)	germline	clinical testing	Citation Link,
SCV002022569	Revvity Omics, Revvity	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (May 28, 2020)	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	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	yes	1	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	2	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Prevalence and mutation spectrum of skeletal muscle channelopathies in the Netherlands.

Stunnenberg BC, Raaphorst J, Deenen JCW, Links TP, Wilde AA, Verbove DJ, Kamsteeg EJ, van den Wijngaard A, Faber CG, van der Wilt GJ, van Engelen BGM, Drost G, Ginjaar HB.

Neuromuscul Disord. 2018 May;28(5):402-407. doi: 10.1016/j.nmd.2018.03.006. Epub 2018 Mar 9.

PubMed [citation]

PMID:: 29606556

Muscle MRI reveals distinct abnormalities in genetically proven non-dystrophic myotonias.

Morrow JM, Matthews E, Raja Rayan DL, Fischmann A, Sinclair CD, Reilly MM, Thornton JS, Hanna MG, Yousry TA.

Neuromuscul Disord. 2013 Aug;23(8):637-46. doi: 10.1016/j.nmd.2013.05.001. Epub 2013 Jun 27.

PubMed [citation]

PMID:: 23810313
PMCID:: PMC3744809

See all PubMed Citations (7)

Details of each submission

From Eurofins Ntd Llc (ga), SCV000343271.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	2	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		2	not provided	not provided	not provided

From Athena Diagnostics, SCV000841568.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (6)

Description

The frequency of this variant in the general population is consistent with pathogenicity. Found in at least one patient with expected phenotype for this gene. Predicted to have a damaging effect on the protein. Located in potentially critical domain of the protein. One other pathogenic or likely pathogenic variant affects the same amino acid. 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.

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

From CeGaT Center for Human Genetics Tuebingen, SCV001248202.22

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

#	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		1	not provided	not provided	not provided

From GeneDx, SCV001822902.1

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

Description

Not observed at a significant frequency in large population cohorts (Lek et al., 2016); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This variant is associated with the following publications: (PMID: 22987687, 32670189, 23810313, 24037712, 24349310, 29606556)

#	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

From Revvity Omics, Revvity, SCV002022569.3

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

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

Last Updated: Jun 17, 2024

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