ClinVar Miner

Submissions for variant NM_003060.4(SLC22A5):c.349T>C (p.Trp117Arg)

gnomAD frequency: 0.00001  dbSNP: rs398123692
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000080054 SCV000111949 uncertain significance not provided 2013-11-19 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001321578 SCV001512414 pathogenic Renal carnitine transport defect 2025-01-22 criteria provided, single submitter clinical testing This sequence change replaces tryptophan, which is neutral and slightly polar, with arginine, which is basic and polar, at codon 117 of the SLC22A5 protein (p.Trp117Arg). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with clinical features of primary carnitine deficiency (internal data). ClinVar contains an entry for this variant (Variation ID: 94100). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is expected to disrupt SLC22A5 protein function with a positive predictive value of 95%. For these reasons, this variant has been classified as Pathogenic.
Genome-Nilou Lab RCV001321578 SCV002055846 uncertain significance Renal carnitine transport defect 2021-07-15 criteria provided, single submitter clinical testing
GeneDx RCV000080054 SCV003195247 uncertain significance not provided 2022-07-18 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
Natera, Inc. RCV002226456 SCV002078299 uncertain significance Decreased circulating carnitine concentration 2020-12-21 no assertion criteria provided clinical testing
Natera, Inc. RCV001321578 SCV002107422 uncertain significance Renal carnitine transport defect 2020-12-21 no assertion criteria provided clinical testing

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