NM_001127898.4(CLCN5):c.1413_1414del (p.Cys471_Asp472delinsTer) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Dec 4, 2022
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:: RCV003713780.2

Allele description [Variation Report for NM_001127898.4(CLCN5):c.1413_1414del (p.Cys471_Asp472delinsTer)]

NM_001127898.4(CLCN5):c.1413_1414del (p.Cys471_Asp472delinsTer)

Gene:

CLCN5:chloride voltage-gated channel 5 [Gene - OMIM - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

Xp11.23

Genomic location:

Preferred name:

NM_001127898.4(CLCN5):c.1413_1414del (p.Cys471_Asp472delinsTer)

HGVS:

NC_000023.11:g.50086724TG[1]
NG_007159.3:g.169109TG[1]
NM_000084.5:c.1203_1204del
NM_001127898.4:c.1413_1414delMANE SELECT
NM_001127899.4:c.1413_1414del
NM_001282163.2:c.1263_1264del
NP_000075.1:p.Cys401_Asp402delinsTer
NP_001121370.1:p.Cys471_Asp472delinsTer
NP_001121371.1:p.Cys471_Asp472delinsTer
NP_001269092.1:p.Cys421_Asp422delinsTer
NC_000023.10:g.49851381TG[1]
NC_000023.10:g.49851381_49851382del
NR_073607.1:n.1492_1493TG[1]

Molecular consequence:

NM_000084.5:c.1203_1204del - nonsense - [Sequence Ontology: SO:0001587]
NM_001127898.4:c.1413_1414del - nonsense - [Sequence Ontology: SO:0001587]
NM_001127899.4:c.1413_1414del - nonsense - [Sequence Ontology: SO:0001587]
NM_001282163.2:c.1263_1264del - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004487514	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Dec 4, 2022)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 32495484, 22876375, 25907713, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004487514

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Dec 4, 2022)

germline

clinical testing

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

Help

Summary from all submissions

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

Citations

PubMed

Phenotypic spectrum and antialbuminuric response to angiotensin converting enzyme inhibitor and angiotensin receptor blocker therapy in pediatric Dent disease.

Deng H, Zhang Y, Xiao H, Yao Y, Zhang H, Liu X, Su B, Guan N, Zhong X, Wang S, Ding J, Wang F.

Mol Genet Genomic Med. 2020 Aug;8(8):e1306. doi: 10.1002/mgg3.1306. Epub 2020 Jun 3.

PubMed [citation]

PMID:: 32495484
PMCID:: PMC7434612

Dent Disease.

Lieske JC, Milliner DS, Beara-Lasic L, Harris P, Cogal A, Abrash E.

2012 Aug 9 [updated 2017 Dec 14]. In: Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE, Amemiya A, editors. GeneReviews(®) [Internet]. Seattle (WA): University of Washington, Seattle; 1993-2024.

PubMed [citation]

PMID:: 22876375

See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004487514.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

For these reasons, this variant has been classified as Pathogenic. This premature translational stop signal has been observed in individual(s) with clinical features consistent with Dent disease (PMID: 32495484). This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Cys401*) in the CLCN5 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in CLCN5 are known to be pathogenic (PMID: 22876375, 25907713).

#	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: Sep 29, 2024

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