ClinVar Miner

Submissions for variant NM_006950.3(SYN1):c.1657T>C (p.Ser553Pro)

gnomAD frequency: 0.00001  dbSNP: rs1165799072
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Centre for Mendelian Genomics, University Medical Centre Ljubljana RCV001216465 SCV001370062 uncertain significance Epilepsy, X-linked 1, with variable learning disabilities and behavior disorders 2016-01-01 criteria provided, single submitter clinical testing This variant was classified as: Uncertain significance. The following ACMG criteria were applied in classifying this variant: PM2,BP4.
Invitae RCV001216465 SCV001388264 uncertain significance Epilepsy, X-linked 1, with variable learning disabilities and behavior disorders 2022-11-18 criteria provided, single submitter clinical testing 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. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Not Available"; Align-GVGD: "Class C0"). ClinVar contains an entry for this variant (Variation ID: 931996). This variant has not been reported in the literature in individuals affected with SYN1-related conditions. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate insufficient coverage at this position in the gnomAD database. This sequence change replaces serine, which is neutral and polar, with proline, which is neutral and non-polar, at codon 553 of the SYN1 protein (p.Ser553Pro).
Ambry Genetics RCV002559271 SCV003546833 uncertain significance Inborn genetic diseases 2022-06-10 criteria provided, single submitter clinical testing The c.1657T>C (p.S553P) alteration is located in exon 12 (coding exon 12) of the SYN1 gene. This alteration results from a T to C substitution at nucleotide position 1657, causing the serine (S) at amino acid position 553 to be replaced by a proline (P). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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