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NM_001127898.4(CLCN5):c.2119C>T (p.Arg707Ter) AND Dent disease

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Oct 26, 2023
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:
RCV003401037.1

Allele description [Variation Report for NM_001127898.4(CLCN5):c.2119C>T (p.Arg707Ter)]

NM_001127898.4(CLCN5):c.2119C>T (p.Arg707Ter)

Genes:
LOC126863258:BRD4-independent group 4 enhancer GRCh37_chrX:49854497-49855696 [Gene]
CLCN5:chloride voltage-gated channel 5 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Xp11.23
Genomic location:
Preferred name:
NM_001127898.4(CLCN5):c.2119C>T (p.Arg707Ter)
HGVS:
  • NC_000023.11:g.50090490C>T
  • NG_007159.3:g.172875C>T
  • NM_000084.5:c.1909C>T
  • NM_001127898.4:c.2119C>TMANE SELECT
  • NM_001127899.4:c.2119C>T
  • NM_001282163.2:c.1969C>T
  • NP_000075.1:p.Arg637Ter
  • NP_001121370.1:p.Arg707Ter
  • NP_001121371.1:p.Arg707Ter
  • NP_001269092.1:p.Arg657Ter
  • NC_000023.10:g.49855147C>T
  • NM_000084.2:c.1909C>T
  • p.R637Ter
Protein change:
R637*
Links:
dbSNP: rs797044813
NCBI 1000 Genomes Browser:
rs797044813
Molecular consequence:
  • NM_000084.5:c.1909C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001127898.4:c.2119C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001127899.4:c.2119C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001282163.2:c.1969C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:
Dent disease
Synonyms:
Dent's disease
Identifiers:
MONDO: MONDO:0015612; MedGen: C0878681; OMIM: PS300009

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004122163Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)		Pathogenic
(Oct 26, 2023) 		germlineclinical testing

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

Citation Link

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Japanese Dent disease has a wider clinical spectrum than Dent disease in Europe/USA: genetic and clinical studies of 86 unrelated patients with low-molecular-weight proteinuria.

Sekine T, Komoda F, Miura K, Takita J, Shimadzu M, Matsuyama T, Ashida A, Igarashi T.

Nephrol Dial Transplant. 2014 Feb;29(2):376-84. doi: 10.1093/ndt/gft394. Epub 2013 Sep 29.

PubMed [citation]
PMID:
24081861

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV004122163.1

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

Description

Variant summary: CLCN5 c.1909C>T (p.Arg637X) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. Variants downstream of this position have been classified as pathogenic in ClinVar. The variant was absent in 175419 control chromosomes (gnomAD). c.1909C>T has been reported in the literature in individuals affected with Dent Disease (example: Sekine_2014). The following publication has been ascertained in the context of this evaluation (PMID: 24081861). Six submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. All submitters classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.

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

Last Updated: Sep 29, 2024