ClinVar Miner

Submissions for variant NM_153240.5(NPHP3):c.3062C>T (p.Ala1021Val)

gnomAD frequency: 0.00006  dbSNP: rs759153335
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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) RCV000348806 SCV000340618 uncertain significance not provided 2016-04-21 criteria provided, single submitter clinical testing
Invitae RCV001360586 SCV001556511 uncertain significance Nephronophthisis 2023-07-03 criteria provided, single submitter clinical testing 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. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt NPHP3 protein function. ClinVar contains an entry for this variant (Variation ID: 286995). This variant has not been reported in the literature in individuals affected with NPHP3-related conditions. This variant is present in population databases (rs759153335, gnomAD 0.02%). This sequence change replaces alanine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 1021 of the NPHP3 protein (p.Ala1021Val).
GeneDx RCV000348806 SCV001993496 uncertain significance not provided 2019-08-21 criteria provided, single submitter clinical testing In silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
Fulgent Genetics, Fulgent Genetics RCV002502141 SCV002812770 uncertain significance Renal-hepatic-pancreatic dysplasia 1; Nephronophthisis 3; NPHP3-related Meckel-like syndrome 2021-12-16 criteria provided, single submitter clinical testing

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