ClinVar Miner

Submissions for variant NM_080632.3(UPF3B):c.277A>G (p.Met93Val)

gnomAD frequency: 0.00004  dbSNP: rs770557726
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
CeGaT Center for Human Genetics Tuebingen RCV001311100 SCV001501143 likely benign not provided 2024-08-01 criteria provided, single submitter clinical testing UPF3B: BS2
Labcorp Genetics (formerly Invitae), Labcorp RCV001871772 SCV002142274 uncertain significance Syndromic X-linked intellectual disability 14 2023-11-19 criteria provided, single submitter clinical testing This sequence change replaces methionine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 93 of the UPF3B protein (p.Met93Val). This variant is present in population databases (rs770557726, gnomAD 0.004%). 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: 1012886). 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.
Ambry Genetics RCV002437065 SCV002747250 uncertain significance Inborn genetic diseases 2018-10-23 criteria provided, single submitter clinical testing The p.M93V variant (also known as c.277A>G), located in coding exon 3 of the UPF3B gene, results from an A to G substitution at nucleotide position 277. The methionine at codon 93 is replaced by valine, an amino acid with highly similar properties. This amino acid position is not 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.

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