ClinVar Miner

Submissions for variant NM_153240.5(NPHP3):c.3237G>C (p.Gln1079His)

gnomAD frequency: 0.00001  dbSNP: rs764287266
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000591070 SCV000705744 uncertain significance not provided 2017-10-05 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000804077 SCV000943971 uncertain significance Nephronophthisis 2022-07-19 criteria provided, single submitter clinical testing This sequence change replaces glutamine, which is neutral and polar, with histidine, which is basic and polar, at codon 1079 of the NPHP3 protein (p.Gln1079His). This variant is present in population databases (rs764287266, gnomAD 0.07%). 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: 499991). 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: "Probably 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.
Fulgent Genetics, Fulgent Genetics RCV002491200 SCV002783726 uncertain significance Renal-hepatic-pancreatic dysplasia 1; Nephronophthisis 3; NPHP3-related Meckel-like syndrome 2021-12-21 criteria provided, single submitter clinical testing
GeneDx RCV000591070 SCV003840711 uncertain significance not provided 2022-09-13 criteria provided, single submitter clinical testing In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
PreventionGenetics, part of Exact Sciences RCV004740354 SCV005357566 uncertain significance NPHP3-related disorder 2024-05-24 no assertion criteria provided clinical testing The NPHP3 c.3237G>C variant is predicted to result in the amino acid substitution p.Gln1079His. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.069% of alleles in individuals of Latino descent in gnomAD. Although we suspect that this variant may be benign, 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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