ClinVar Miner

Submissions for variant NM_203446.3(SYNJ1):c.2505C>A (p.Ser835Arg)

gnomAD frequency: 0.00001  dbSNP: rs748032685
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
CeGaT Center for Human Genetics Tuebingen RCV000997820 SCV001153542 uncertain significance not provided 2023-08-01 criteria provided, single submitter clinical testing SYNJ1: PM2
Invitae RCV001042341 SCV001206018 uncertain significance Early-onset Parkinson disease 20; Developmental and epileptic encephalopathy, 53 2022-10-27 criteria provided, single submitter clinical testing This variant is present in population databases (rs748032685, gnomAD 0.004%). This sequence change replaces serine, which is neutral and polar, with arginine, which is basic and polar, at codon 874 of the SYNJ1 protein (p.Ser874Arg). This variant has not been reported in the literature in individuals affected with SYNJ1-related conditions. 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. 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 SYNJ1 protein function. ClinVar contains an entry for this variant (Variation ID: 809282).
Centre for Mendelian Genomics, University Medical Centre Ljubljana RCV001197985 SCV001368770 uncertain significance Developmental and epileptic encephalopathy, 53 2019-04-01 criteria provided, single submitter clinical testing This variant was classified as: Uncertain significance. The available evidence favors the pathogenic nature of this variant, however the currently available data is insufficient to conclusively support its pathogenic nature. Thus this variant is classified as Uncertain significance - favor pathogenic. The following ACMG criteria were applied in classifying this variant: PM2.
Ambry Genetics RCV002549984 SCV003543519 uncertain significance Inborn genetic diseases 2022-09-22 criteria provided, single submitter clinical testing The c.2622C>A (p.S874R) alteration is located in exon 20 (coding exon 20) of the SYNJ1 gene. This alteration results from a C to A substitution at nucleotide position 2622, causing the serine (S) at amino acid position 874 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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