ClinVar Miner

Submissions for variant NM_015102.5(NPHP4):c.4106C>T (p.Pro1369Leu)

gnomAD frequency: 0.00003  dbSNP: rs746256511
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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) RCV000595353 SCV000705986 uncertain significance not provided 2018-06-19 criteria provided, single submitter clinical testing
Invitae RCV001234755 SCV001407414 uncertain significance Nephronophthisis 2022-06-13 criteria provided, single submitter clinical testing This sequence change replaces proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 1369 of the NPHP4 protein (p.Pro1369Leu). This variant is present in population databases (rs746256511, 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: 500165). 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.
Ambry Genetics RCV003160035 SCV003894805 uncertain significance Inborn genetic diseases 2023-02-14 criteria provided, single submitter clinical testing The c.4106C>T (p.P1369L) alteration is located in exon 29 (coding exon 28) of the NPHP4 gene. This alteration results from a C to T substitution at nucleotide position 4106, causing the proline (P) at amino acid position 1369 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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