ClinVar Miner

Submissions for variant NM_003060.4(SLC22A5):c.28T>C (p.Phe10Leu)

gnomAD frequency: 0.00001  dbSNP: rs759420042
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV002026760 SCV002307633 uncertain significance Renal carnitine transport defect 2022-10-24 criteria provided, single submitter clinical testing This sequence change replaces phenylalanine, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 10 of the SLC22A5 protein (p.Phe10Leu). This variant is present in population databases (rs759420042, gnomAD 0.002%). This variant has not been reported in the literature in individuals affected with SLC22A5-related conditions. ClinVar contains an entry for this variant (Variation ID: 1516651). 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 SLC22A5 protein function. 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.
Giacomini Lab, University of California, San Francisco RCV002026760 SCV002576612 uncertain significance Renal carnitine transport defect 2022-10-03 criteria provided, single submitter research
Neuberg Centre For Genomic Medicine, NCGM RCV002026760 SCV005060913 uncertain significance Renal carnitine transport defect criteria provided, single submitter clinical testing The missense variant c.28T>C(p.Phe10Leu) in SLC22A5 gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The observed variant has allele frequency of 0.0008% in gnomAD exomes database. This variant has been submitted to the ClinVar database as Uncertain Significance. The amino acid change p.Phe10Leu in SLC22A5 is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. The amino acid Phe at position 10 is changed to a Leu changing protein sequence and it might alter its composition and physico-chemical properties. For these reasons, this variant has been classified as Uncertain Significance (VUS).
Ambry Genetics RCV004671624 SCV005171714 uncertain significance Inborn genetic diseases 2024-05-08 criteria provided, single submitter clinical testing The c.28T>C (p.F10L) alteration is located in exon 1 (coding exon 1) of the SLC22A5 gene. This alteration results from a T to C substitution at nucleotide position 28, causing the phenylalanine (F) at amino acid position 10 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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