ClinVar Miner

Submissions for variant NM_003060.4(SLC22A5):c.113C>A (p.Ser38Tyr)

gnomAD frequency: 0.00001  dbSNP: rs369354736
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001346970 SCV001541208 pathogenic Renal carnitine transport defect 2024-01-11 criteria provided, single submitter clinical testing This sequence change replaces serine, which is neutral and polar, with tyrosine, which is neutral and polar, at codon 38 of the SLC22A5 protein (p.Ser38Tyr). This variant is present in population databases (rs369354736, gnomAD 0.003%). This missense change has been observed in individual(s) with clinical features of primary carnitine deficiency (Invitae). 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: 1042938). 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) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on SLC22A5 protein function. This variant disrupts the p.Ser38 amino acid residue in SLC22A5. Other variant(s) that disrupt this residue have been determined to be pathogenic (Invitae). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic.
Natera, Inc. RCV002226543 SCV002075432 uncertain significance Decreased circulating carnitine concentration 2021-02-08 no assertion criteria provided clinical testing
Natera, Inc. RCV001346970 SCV002107426 uncertain significance Renal carnitine transport defect 2021-02-08 no assertion criteria provided clinical testing

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