ClinVar Miner

Submissions for variant NM_153240.5(NPHP3):c.2266C>T (p.Arg756Trp)

gnomAD frequency: 0.00006  dbSNP: rs183049702
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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) RCV000592930 SCV000703008 uncertain significance not provided 2016-10-24 criteria provided, single submitter clinical testing
Invitae RCV001867930 SCV002154734 uncertain significance Nephronophthisis 2022-09-27 criteria provided, single submitter clinical testing ClinVar contains an entry for this variant (Variation ID: 498139). This variant has not been reported in the literature in individuals affected with NPHP3-related conditions. This variant is present in population databases (rs183049702, gnomAD 0.02%). This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 756 of the NPHP3 protein (p.Arg756Trp). 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. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. 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.
Fulgent Genetics, Fulgent Genetics RCV002483590 SCV002787793 uncertain significance Renal-hepatic-pancreatic dysplasia 1; Nephronophthisis 3; NPHP3-related Meckel-like syndrome 2021-12-09 criteria provided, single submitter clinical testing
Ambry Genetics RCV003243206 SCV003965024 uncertain significance Inborn genetic diseases 2023-05-05 criteria provided, single submitter clinical testing The c.2266C>T (p.R756W) alteration is located in exon 16 (coding exon 16) of the NPHP3 gene. This alteration results from a C to T substitution at nucleotide position 2266, causing the arginine (R) at amino acid position 756 to be replaced by a tryptophan (W). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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