ClinVar Miner

Submissions for variant NM_153240.5(NPHP3):c.273del (p.Glu90_Tyr91insTer)

dbSNP: rs758558609
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000173578 SCV000224702 pathogenic not provided 2014-06-18 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001390246 SCV001591916 pathogenic Nephronophthisis 2024-07-20 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Tyr91*) in the NPHP3 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in NPHP3 are known to be pathogenic (PMID: 18371931, 23559409). This variant is present in population databases (rs758558609, gnomAD 0.0009%). This variant has not been reported in the literature in individuals affected with NPHP3-related conditions. ClinVar contains an entry for this variant (Variation ID: 193505). For these reasons, this variant has been classified as Pathogenic.
GeneDx RCV000173578 SCV004031914 likely pathogenic not provided 2023-03-01 criteria provided, single submitter clinical testing Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss of function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 31980526)
PreventionGenetics, part of Exact Sciences RCV004539598 SCV004787979 pathogenic NPHP3-related disorder 2023-12-12 no assertion criteria provided clinical testing The NPHP3 c.273delC variant is predicted to result in premature protein termination (p.Tyr91*). To our knowledge, this variant has not been reported in the literature in any individuals with an NPHP3-related disorder. This variant is reported in 0.00091% of alleles in individuals of European (non-Finnish) descent in gnomAD. Nonsense variants in NPHP3 are expected to be pathogenic. This variant is interpreted as pathogenic.

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