ClinVar Miner

Submissions for variant NM_015102.5(NPHP4):c.1585G>A (p.Gly529Ser)

gnomAD frequency: 0.00002  dbSNP: rs750626428
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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) RCV000734927 SCV000863107 uncertain significance not provided 2018-08-23 criteria provided, single submitter clinical testing
Genome Diagnostics Laboratory, The Hospital for Sick Children RCV002294375 SCV002587547 uncertain significance Kidney disorder 2016-12-12 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV002485946 SCV002793108 uncertain significance Nephronophthisis 4; Senior-Loken syndrome 4 2022-03-19 criteria provided, single submitter clinical testing
Invitae RCV002535402 SCV003241390 uncertain significance Nephronophthisis 2022-07-20 criteria provided, single submitter clinical testing This variant is present in population databases (rs750626428, gnomAD 0.005%). This sequence change replaces glycine, which is neutral and non-polar, with serine, which is neutral and polar, at codon 529 of the NPHP4 protein (p.Gly529Ser). This variant has not been reported in the literature in individuals affected with NPHP4-related conditions. 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 create or strengthen a splice site. Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The serine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. ClinVar contains an entry for this variant (Variation ID: 598518).

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