ClinVar Miner

Submissions for variant NM_002519.3(NPAT):c.3088A>G (p.Lys1030Glu)

gnomAD frequency: 0.00002  dbSNP: rs770282833
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Genetic Services Laboratory, University of Chicago RCV001818077 SCV002067848 uncertain significance not specified 2021-09-21 criteria provided, single submitter clinical testing This sequence change does not appear to have been previously described in patients with NPAT-related disorders and has been described in the gnomAD database with a low population frequency of 0.0047% in the non-Finnish subpopulation (dbSNP rs770282833). The p.Lys1030Glu change affects a highly conserved amino acid residue located in a domain of the NPAT protein that is not known to be functional. In-silico pathogenicity prediction tools (SIFT, PolyPhen2, Align GVGD, REVEL) provide contradictory results for the p.Lys1030Glu substitution. Due to this insufficient evidence and the lack of functional studies, the clinical significance of the p.Lys1030Glu change remains unknown at this time.
Ambry Genetics RCV001818077 SCV003911098 uncertain significance not specified 2023-01-28 criteria provided, single submitter clinical testing The p.K1030E variant (also known as c.3088A>G), located in coding exon 17 of the NPAT gene, results from an A to G substitution at nucleotide position 3088. The lysine at codon 1030 is replaced by glutamic acid, an amino acid with similar properties. This amino acid position is conserved. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
Labcorp Genetics (formerly Invitae), Labcorp RCV003718446 SCV004519110 uncertain significance not provided 2023-12-17 criteria provided, single submitter clinical testing This sequence change replaces lysine, which is basic and polar, with glutamic acid, which is acidic and polar, at codon 1030 of the NPAT protein (p.Lys1030Glu). This variant is present in population databases (rs770282833, gnomAD 0.004%). This variant has not been reported in the literature in individuals affected with NPAT-related conditions. ClinVar contains an entry for this variant (Variation ID: 1338706). 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.

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