ClinVar Miner

Submissions for variant NM_080632.3(UPF3B):c.388A>G (p.Ile130Val)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV002357383 SCV002620589 uncertain significance Inborn genetic diseases 2017-12-15 criteria provided, single submitter clinical testing The p.I130V variant (also known as c.388A>G), located in coding exon 4 of the UPF3B gene, results from an A to G substitution at nucleotide position 388. The isoleucine at codon 130 is replaced by valine, an amino acid with highly similar properties. This amino acid position is well conserved in available vertebrate species. 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 RCV003094429 SCV003211309 uncertain significance Syndromic X-linked intellectual disability 14 2024-01-18 criteria provided, single submitter clinical testing This sequence change replaces isoleucine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 130 of the UPF3B protein (p.Ile130Val). This variant is present in population databases (rs201112408, gnomAD 0.006%). This variant has not been reported in the literature in individuals affected with UPF3B-related conditions. ClinVar contains an entry for this variant (Variation ID: 1735870). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt UPF3B protein function with a negative predictive value of 80%. 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.
Revvity Omics, Revvity RCV003094429 SCV003828066 uncertain significance Syndromic X-linked intellectual disability 14 2021-10-01 criteria provided, single submitter clinical testing

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