ClinVar Miner

Submissions for variant NM_018230.3(NUP133):c.3164T>C (p.Leu1055Ser)

gnomAD frequency: 0.00006  dbSNP: rs376476266
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
SIB Swiss Institute of Bioinformatics RCV000721159 SCV000899129 likely pathogenic Nephrotic syndrome, type 18 2019-01-10 criteria provided, single submitter curation This variant is interpreted as a Likely pathogenic for Nephrotic syndrome 18, autosomal recessive. The following ACMG Tag(s) were applied: PM2 => Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium. PS3 => Well-established functional studies show a deleterious effect (PMID:30179222). PP1 => Cosegregation with disease in multiple affected family members in a gene definitively known to cause the disease (PMID:30179222). PP3 => Multiple lines of computational evidence support a deleterious effect on the gene or gene product.
Invitae RCV003718283 SCV004507096 uncertain significance not provided 2023-12-11 criteria provided, single submitter clinical testing This sequence change replaces leucine, which is neutral and non-polar, with serine, which is neutral and polar, at codon 1055 of the NUP133 protein (p.Leu1055Ser). This variant is present in population databases (rs376476266, gnomAD 0.01%). This missense change has been observed in individual(s) with clinical features of nephrotic syndrome (PMID: 30179222). ClinVar contains an entry for this variant (Variation ID: 590320). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. 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.
OMIM RCV000721159 SCV000852072 pathogenic Nephrotic syndrome, type 18 2018-11-12 no assertion criteria provided literature only

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