ClinVar Miner

Submissions for variant NM_015102.5(NPHP4):c.3757C>T (p.Arg1253Trp)

gnomAD frequency: 0.00005  dbSNP: rs762195159
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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) RCV000310947 SCV000340019 uncertain significance not provided 2016-02-25 criteria provided, single submitter clinical testing
Invitae RCV001235811 SCV001408516 uncertain significance Nephronophthisis 2022-07-19 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 1253 of the NPHP4 protein (p.Arg1253Trp). This variant is present in population databases (rs762195159, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with NPHP4-related conditions. ClinVar contains an entry for this variant (Variation ID: 286539). 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 RCV002487237 SCV002793480 uncertain significance Nephronophthisis 4; Senior-Loken syndrome 4 2021-11-16 criteria provided, single submitter clinical testing
Ambry Genetics RCV003258728 SCV003948264 uncertain significance Inborn genetic diseases 2023-05-22 criteria provided, single submitter clinical testing The c.3757C>T (p.R1253W) alteration is located in exon 27 (coding exon 26) of the NPHP4 gene. This alteration results from a C to T substitution at nucleotide position 3757, causing the arginine (R) at amino acid position 1253 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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