ClinVar Miner

Submissions for variant NM_025243.4(SLC19A3):c.541T>C (p.Ser181Pro)

gnomAD frequency: 0.00006  dbSNP: rs773971505
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München RCV000578309 SCV000680375 pathogenic Biotin-responsive basal ganglia disease 2017-12-11 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000578309 SCV004294034 pathogenic Biotin-responsive basal ganglia disease 2023-11-17 criteria provided, single submitter clinical testing This sequence change replaces serine, which is neutral and polar, with proline, which is neutral and non-polar, at codon 181 of the SLC19A3 protein (p.Ser181Pro). This variant is present in population databases (rs773971505, gnomAD 0.07%). This missense change has been observed in individual(s) with clinical features of biotin-responsive basal ganglia disease (PMID: 23482991, 26863430, 28856750). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 488596). 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 with a positive predictive value of 80%. For these reasons, this variant has been classified as Pathogenic.

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