ClinVar Miner

Submissions for variant NM_153240.5(NPHP3):c.233G>T (p.Gly78Val) (rs202142404)

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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics RCV000726607 SCV000345803 uncertain significance not provided 2016-09-01 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000283485 SCV000441157 uncertain significance Nephronophthisis 2016-06-14 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000343202 SCV000441158 uncertain significance Renal-hepatic-pancreatic dysplasia 1 2016-06-14 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000404760 SCV000441159 uncertain significance Meckel-Gruber syndrome 2016-06-14 criteria provided, single submitter clinical testing
GeneDx RCV000726607 SCV000590321 uncertain significance not provided 2017-06-13 criteria provided, single submitter clinical testing A variant of uncertain significance has been identified in the NPHP3 gene. The G78V variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The G78V variant is observed in 1/8252 (0.01%) alleles from individuals of East Asian background (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). The G78V variant is a conservative amino acid substitution, which is not likely to impact secondary protein structure as these residues share similar properties. This substitution occurs at a position where amino acids with similar properties to Glycine are tolerated across species. However, in silico analysis predicts this variant is probably damaging to the protein structure/function. Therefore, based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant.
Invitae RCV000283485 SCV000831174 uncertain significance Nephronophthisis 2019-12-05 criteria provided, single submitter clinical testing This sequence change replaces glycine with valine at codon 78 of the NPHP3 protein (p.Gly78Val). The glycine residue is moderately conserved and there is a moderate physicochemical difference between glycine and valine. This variant is present in population databases (rs202142404, ExAC 0.01%). This variant has not been reported in the literature in individuals with NPHP3-related disease. ClinVar contains an entry for this variant (Variation ID: 291105). 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: "Benign"; 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.

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