ClinVar Miner

Submissions for variant NM_152594.3(SPRED1):c.47G>A (p.Arg16Gln)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001880007 SCV002222308 uncertain significance Legius syndrome 2023-09-06 criteria provided, single submitter clinical testing This variant is present in population databases (rs757726772, gnomAD 0.003%). This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 16 of the SPRED1 protein (p.Arg16Gln). This variant has not been reported in the literature in individuals affected with SPRED1-related conditions. ClinVar contains an entry for this variant (Variation ID: 981594). 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 SPRED1 protein function. 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.
GeneDx RCV003442818 SCV004169902 uncertain significance not provided 2023-05-09 criteria provided, single submitter clinical testing Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
Ambry Genetics RCV004035385 SCV005030827 uncertain significance Cardiovascular phenotype 2024-01-27 criteria provided, single submitter clinical testing The p.R16Q variant (also known as c.47G>A), located in coding exon 2 of the SPRED1 gene, results from a G to A substitution at nucleotide position 47. The arginine at codon 16 is replaced by glutamine, an amino acid with highly similar properties. This amino acid position is conserved. In addition, the in silico prediction for this alteration is inconclusive. Based on the available evidence, the clinical significance of this alteration remains unclear.
Service de Génétique Moléculaire, Hôpital Robert Debré RCV001261129 SCV001438536 uncertain significance Noonan syndrome no assertion criteria provided clinical testing

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