ClinVar Miner

Submissions for variant NM_002519.3(NPAT):c.1232A>T (p.Glu411Val)

gnomAD frequency: 0.00038  dbSNP: rs201010866
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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 RCV001820457 SCV002071366 likely benign not specified 2019-11-12 criteria provided, single submitter clinical testing
Ambry Genetics RCV001820457 SCV002666065 uncertain significance not specified 2024-02-28 criteria provided, single submitter clinical testing The c.1232A>T (p.E411V) alteration is located in exon 13 (coding exon 13) of the NPAT gene. This alteration results from a A to T substitution at nucleotide position 1232, causing the glutamic acid (E) at amino acid position 411 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
Labcorp Genetics (formerly Invitae), Labcorp RCV003565498 SCV004317384 uncertain significance not provided 2024-11-11 criteria provided, single submitter clinical testing This sequence change replaces glutamic acid, which is acidic and polar, with valine, which is neutral and non-polar, at codon 411 of the NPAT protein (p.Glu411Val). This variant is present in population databases (rs201010866, gnomAD 0.1%), and has an allele count higher than expected for a pathogenic variant. 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: 1337443). 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. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. 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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