ClinVar Miner

Submissions for variant NM_152594.3(SPRED1):c.6C>A (p.Ser2Arg)

gnomAD frequency: 0.00001  dbSNP: rs775693385
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001239829 SCV001412730 uncertain significance Legius syndrome 2023-11-22 criteria provided, single submitter clinical testing This sequence change replaces serine, which is neutral and polar, with arginine, which is basic and polar, at codon 2 of the SPRED1 protein (p.Ser2Arg). This variant is not present in population databases (gnomAD no frequency). 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: 965391). 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 tolerated. 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.
Baylor Genetics RCV001239829 SCV001523892 uncertain significance Legius syndrome 2020-01-31 criteria provided, single submitter clinical testing This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868].
New York Genome Center RCV001239829 SCV002097805 uncertain significance Legius syndrome 2021-02-11 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV001239829 SCV002775816 uncertain significance Legius syndrome 2021-10-16 criteria provided, single submitter clinical testing
Ambry Genetics RCV003166494 SCV003868990 uncertain significance Cardiovascular phenotype 2022-12-16 criteria provided, single submitter clinical testing The p.S2R variant (also known as c.6C>A), located in coding exon 1 of the SPRED1 gene, results from a C to A substitution at nucleotide position 6. The serine at codon 2 is replaced by arginine, an amino acid with dissimilar properties. This amino acid position is conserved. 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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