ClinVar Miner

Submissions for variant NM_153240.5(NPHP3):c.3499C>T (p.Arg1167Cys)

gnomAD frequency: 0.00001  dbSNP: rs201135796
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000704419 SCV000833368 uncertain significance Nephronophthisis 2022-09-07 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 1167 of the NPHP3 protein (p.Arg1167Cys). This variant is present in population databases (rs201135796, gnomAD 0.008%). 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: 580774). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Eurofins Ntd Llc (ga) RCV000732403 SCV000860360 uncertain significance not provided 2018-03-15 criteria provided, single submitter clinical testing
GeneDx RCV000732403 SCV002001989 uncertain significance not provided 2020-02-10 criteria provided, single submitter clinical testing Not observed at a significant frequency in large population cohorts (Lek et al., 2016); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
Fulgent Genetics, Fulgent Genetics RCV002493237 SCV002791445 uncertain significance Renal-hepatic-pancreatic dysplasia 1; Nephronophthisis 3; NPHP3-related Meckel-like syndrome 2022-03-16 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV003411641 SCV004115954 uncertain significance NPHP3-related condition 2023-04-21 criteria provided, single submitter clinical testing The NPHP3 c.3499C>T variant is predicted to result in the amino acid substitution p.Arg1167Cys. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.0080% of alleles in individuals of African descent in gnomAD (http://gnomad.broadinstitute.org/variant/3-132403469-G-A). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

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