ClinVar Miner

Submissions for variant NM_003060.4(SLC22A5):c.1A>G (p.Met1Val)

dbSNP: rs774971089
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000669076 SCV000793778 likely pathogenic Renal carnitine transport defect 2017-08-30 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000669076 SCV005808388 pathogenic Renal carnitine transport defect 2024-02-02 criteria provided, single submitter clinical testing This sequence change affects the initiator methionine of the SLC22A5 mRNA. The next in-frame methionine is located at codon 177. This variant is not present in population databases (gnomAD no frequency). Disruption of the initiator codon has been observed in individual(s) with primary carnitine deficiency (PMID: 15714519). ClinVar contains an entry for this variant (Variation ID: 553595). Algorithms developed to predict the effect of variants on protein structure and function are not available or were not evaluated for this variant. Experimental studies have shown that disruption of the initiator codon affects SLC22A5 function (PMID: 15714519). This variant disrupts a region of the SLC22A5 protein in which other variant(s) (p.Phe17Leu) have been determined to be pathogenic (PMID: 16931768, 20074989, 20574985, 25132046). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic.

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