ClinVar Miner

Submissions for variant NM_203446.3(SYNJ1):c.2786T>C (p.Ile929Thr)

gnomAD frequency: 0.00001  dbSNP: rs755258923
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000655756 SCV000777687 uncertain significance Early-onset Parkinson disease 20; Developmental and epileptic encephalopathy, 53 2022-08-22 criteria provided, single submitter clinical testing This sequence change replaces isoleucine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 968 of the SYNJ1 protein (p.Ile968Thr). This variant is present in population databases (rs755258923, gnomAD 0.003%). This variant has not been reported in the literature in individuals affected with SYNJ1-related conditions. ClinVar contains an entry for this variant (Variation ID: 544559). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The threonine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect 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 RCV002473097 SCV002769988 uncertain significance not provided 2022-06-21 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 RCV002536308 SCV003554984 uncertain significance Inborn genetic diseases 2022-05-01 criteria provided, single submitter clinical testing The c.2903T>C (p.I968T) alteration is located in exon 21 (coding exon 21) of the SYNJ1 gene. This alteration results from a T to C substitution at nucleotide position 2903, causing the isoleucine (I) at amino acid position 968 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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