ClinVar Miner

Submissions for variant NM_152594.3(SPRED1):c.563T>C (p.Met188Thr)

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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 RCV004035386 SCV003538065 uncertain significance Cardiovascular phenotype 2024-03-21 criteria provided, single submitter clinical testing The p.M188T variant (also known as c.563T>C), located in coding exon 5 of the SPRED1 gene, results from a T to C substitution at nucleotide position 563. The methionine at codon 188 is replaced by threonine, 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. Based on the available evidence, the clinical significance of this alteration remains unclear.
Labcorp Genetics (formerly Invitae), Labcorp RCV003770354 SCV004631454 uncertain significance Legius syndrome 2024-02-16 criteria provided, single submitter clinical testing This sequence change replaces methionine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 188 of the SPRED1 protein (p.Met188Thr). This variant is present in population databases (rs370735097, gnomAD 0.004%). 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: 981596). 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 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.
Service de Génétique Moléculaire, Hôpital Robert Debré RCV001261132 SCV001438539 uncertain significance Costello syndrome no assertion criteria provided clinical testing

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