ClinVar Miner

Submissions for variant NM_025243.4(SLC19A3):c.488C>T (p.Ser163Phe)

gnomAD frequency: 0.00002  dbSNP: rs898880170
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV001767876 SCV001999693 uncertain significance not provided 2020-01-13 criteria provided, single submitter clinical testing Not observed at a significant frequency in large population cohorts (Lek et al., 2016); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; Has not been previously published as pathogenic or benign to our knowledge
Labcorp Genetics (formerly Invitae), Labcorp RCV003120675 SCV003784308 uncertain significance Biotin-responsive basal ganglia disease 2022-05-13 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. 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 expected to disrupt SLC19A3 protein function. This sequence change replaces serine, which is neutral and polar, with phenylalanine, which is neutral and non-polar, at codon 163 of the SLC19A3 protein (p.Ser163Phe). This variant is present in population databases (no rsID available, gnomAD 0.007%). This variant has not been reported in the literature in individuals affected with SLC19A3-related conditions. ClinVar contains an entry for this variant (Variation ID: 1310762).

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