ClinVar Miner

Submissions for variant NM_015102.5(NPHP4):c.2620G>A (p.Val874Met)

gnomAD frequency: 0.00002  dbSNP: rs1412960310
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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) RCV000596137 SCV000705972 uncertain significance not provided 2018-04-19 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV002476312 SCV002778215 uncertain significance Nephronophthisis 4; Senior-Loken syndrome 4 2022-02-10 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV002531061 SCV003450548 uncertain significance Nephronophthisis 2022-08-10 criteria provided, single submitter clinical testing 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 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"). ClinVar contains an entry for this variant (Variation ID: 500153). This variant has not been reported in the literature in individuals affected with NPHP4-related conditions. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This sequence change replaces valine, which is neutral and non-polar, with methionine, which is neutral and non-polar, at codon 874 of the NPHP4 protein (p.Val874Met).
Ambry Genetics RCV004024780 SCV004990992 uncertain significance Inborn genetic diseases 2024-03-01 criteria provided, single submitter clinical testing The c.2620G>A (p.V874M) alteration is located in exon 20 (coding exon 19) of the NPHP4 gene. This alteration results from a G to A substitution at nucleotide position 2620, causing the valine (V) at amino acid position 874 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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