ClinVar Miner

Submissions for variant NM_003060.4(SLC22A5):c.1409C>T (p.Ser470Phe)

gnomAD frequency: 0.00001  dbSNP: rs386134222
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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics RCV000513827 SCV000610106 pathogenic not provided 2017-06-19 criteria provided, single submitter clinical testing
Counsyl RCV000022381 SCV000799728 uncertain significance Renal carnitine transport defect 2018-05-03 criteria provided, single submitter clinical testing
CeGaT Center for Human Genetics Tuebingen RCV000513827 SCV001247715 pathogenic not provided 2019-02-01 criteria provided, single submitter clinical testing
Invitae RCV000022381 SCV001416144 pathogenic Renal carnitine transport defect 2023-08-02 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. Experimental studies have shown that this missense change affects SLC22A5 function (PMID: 28841266). 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. ClinVar contains an entry for this variant (Variation ID: 25425). This missense change has been observed in individual(s) with carnitine deficiency (PMID: 12210323). This variant is present in population databases (rs386134222, gnomAD 0.006%). This sequence change replaces serine, which is neutral and polar, with phenylalanine, which is neutral and non-polar, at codon 470 of the SLC22A5 protein (p.Ser470Phe).
Centogene AG - the Rare Disease Company RCV000022381 SCV001424486 pathogenic Renal carnitine transport defect criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV000022381 SCV002055779 likely pathogenic Renal carnitine transport defect 2021-07-15 criteria provided, single submitter clinical testing
Giacomini Lab, University of California, San Francisco RCV000022381 SCV002576583 likely pathogenic Renal carnitine transport defect 2022-10-03 criteria provided, single submitter research
Baylor Genetics RCV000022381 SCV004203600 likely pathogenic Renal carnitine transport defect 2022-01-04 criteria provided, single submitter clinical testing

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