ClinVar Miner

Submissions for variant NM_003098.3(SNTA1):c.233C>T (p.Pro78Leu)

gnomAD frequency: 0.00003  dbSNP: rs1241571413
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000520269 SCV000616965 uncertain significance not provided 2017-11-01 criteria provided, single submitter clinical testing A variant of uncertain significance has been identified in the SNTA1 gene. The P78L variant has not been published as pathogenic or been reported as benign to our knowledge. This variant is not observed in large population cohorts (Lek et al., 2016). The P78L variant is a semi-conservative amino acid substitution, which may impact secondary protein structure as these residues differ in some properties. This substitution occurs at a position that is conserved across species. In silico analysis predicts this variant is probably damaging to the protein structure/function. However, this variant lacks observation in a significant number of affected individuals, segregation data, and functional evidence, which would further clarify its pathogenicity.
Invitae RCV002525110 SCV003293890 uncertain significance Long QT syndrome 2022-05-21 criteria provided, single submitter clinical testing The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. 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: "Possibly Damaging"; Align-GVGD: "Class C0"). ClinVar contains an entry for this variant (Variation ID: 449151). This variant has not been reported in the literature in individuals affected with SNTA1-related conditions. This sequence change replaces proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 78 of the SNTA1 protein (p.Pro78Leu).

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