ClinVar Miner

Submissions for variant NM_003060.4(SLC22A5):c.1006C>T (p.Arg336Ter)

gnomAD frequency: 0.00001  dbSNP: rs754008420
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001246766 SCV001420148 pathogenic Renal carnitine transport defect 2025-01-27 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Arg336*) in the SLC22A5 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in SLC22A5 are known to be pathogenic (PMID: 9916797). This variant is present in population databases (rs754008420, gnomAD 0.003%). 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: 971074). For these reasons, this variant has been classified as Pathogenic.
CeGaT Center for Human Genetics Tuebingen RCV002512148 SCV002821315 pathogenic not provided 2022-12-01 criteria provided, single submitter clinical testing SLC22A5: PVS1, PM2
Revvity Omics, Revvity RCV001246766 SCV003816419 likely pathogenic Renal carnitine transport defect 2022-04-27 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV001246766 SCV003922886 likely pathogenic Renal carnitine transport defect 2023-03-23 criteria provided, single submitter clinical testing Variant summary: SLC22A5 c.1006C>T (p.Arg336X) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. Truncations downstream of this position have been classified as pathogenic by our laboratory. The variant allele was found at a frequency of 8e-06 in 251462 control chromosomes (gnomAD). c.1006C>T has been reported in the literature in a compound heterozygous individual affected with Systemic Primary Carnitine Deficiency (Louis_2023). To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Three clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014, and classified the variant as pathogenic (n=2) or likely pathogenic (n=1). Based on the evidence outlined above, the variant was classified as likely pathogenic.
Baylor Genetics RCV001246766 SCV004203570 likely pathogenic Renal carnitine transport defect 2024-02-07 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV001246766 SCV005669222 pathogenic Renal carnitine transport defect 2024-03-20 criteria provided, single submitter clinical testing

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