ClinVar Miner

Submissions for variant NM_001127898.4(CLCN5):c.310C>T (p.Arg104Ter)

dbSNP: rs797044808
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
PreventionGenetics, part of Exact Sciences RCV003417691 SCV004112947 pathogenic CLCN5-related disorder 2022-12-07 criteria provided, single submitter clinical testing The CLCN5 c.100C>T variant is predicted to result in premature protein termination (p.Arg34*). This variant has been reported to have occurred de novo or be inherited from a mother with nephrolithiasis in two hemizygous patients with Dent disease (Hoopes et al. 1998. PubMed ID: 9734595; Wen et al. 2018. PubMed ID: 30581818). This variant has not been reported in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. Nonsense variants in CLCN5 are expected to be pathogenic. This variant is interpreted as pathogenic.
Neuberg Centre For Genomic Medicine, NCGM RCV004546452 SCV005042922 likely pathogenic Familial X-linked hypophosphatemic vitamin D refractory rickets criteria provided, single submitter clinical testing The stop gained c.310C>Tp.Arg104Ter variant in CLCN5 gene has reported in hemizygous state in an individual affected with CLCN5 related disorders Wen M, et. al., 2018. The c.310C>T variant is novel not in any individuals in gnomAD Exomes and 1000Genomes. This variant has been reported to the ClinVar database. The nucleotide change c.310C>T in CLCN5 is predicted asconserved by GERP++ and PhyloP across 100 vertebrates. Loss of function variants have been previously reported to be diseasecausing. For these reasons, this variant has been classified as Likely Pathogenic.
GeneReviews RCV000192273 SCV000243781 not provided Dent disease type 1 no assertion provided literature only

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