ClinVar Miner

Submissions for variant NM_001128178.3(NPHP1):c.493G>A (p.Ala165Thr)

gnomAD frequency: 0.00009  dbSNP: rs377676279
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000597926 SCV000703613 uncertain significance not provided 2016-12-19 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001300113 SCV001489237 uncertain significance Nephronophthisis 2022-08-23 criteria provided, single submitter clinical testing This sequence change replaces alanine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 165 of the NPHP1 protein (p.Ala165Thr). This variant is present in population databases (rs377676279, gnomAD 0.05%). This variant has not been reported in the literature in individuals affected with NPHP1-related conditions. ClinVar contains an entry for this variant (Variation ID: 498548). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Deleterious"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0". The threonine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. 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 RCV002483593 SCV002790955 uncertain significance Joubert syndrome with renal defect; Nephronophthisis 1; Senior-Loken syndrome 1 2022-01-27 criteria provided, single submitter clinical testing

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