Total submissions: 5
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 |
RCV000732403 | SCV000860360 | uncertain significance | not provided | 2018-03-15 | criteria provided, single submitter | clinical testing | |
Gene |
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, |
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 | |
Prevention |
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. |