ClinVar Miner

Submissions for variant NM_003060.4(SLC22A5):c.1250dup (p.Met417fs)

gnomAD frequency: 0.00001  dbSNP: rs781330134
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000599514 SCV000709849 likely pathogenic not provided 2018-09-13 criteria provided, single submitter clinical testing The c.1250dupT variant in the SLC22A5 gene causes a frameshift starting with codon Methionine 417, changes this amino acid to a Isoleucine residue and creates a premature Stop codon at position 106 of the new reading frame, denoted p.Met417IlefsX106. This variant is predicted to cause loss of normal protein function through protein truncation. Although this variant has not been previously reported to our knowledge, it is interpreted to be a likely pathogenic variant.
Invitae RCV000635351 SCV000756756 pathogenic Renal carnitine transport defect 2024-01-08 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Met417Ilefs*106) in the SLC22A5 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 141 amino acid(s) of the SLC22A5 protein. This variant is present in population databases (rs781330134, gnomAD 0.0009%). 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: 503649). This variant disrupts a region of the SLC22A5 protein in which other variant(s) (p.Asp519Thrfs*7) have been determined to be pathogenic (Invitae). 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.
Baylor Genetics RCV000635351 SCV004203579 likely pathogenic Renal carnitine transport defect 2023-03-16 criteria provided, single submitter clinical testing
Counsyl RCV000635351 SCV001132287 likely pathogenic Renal carnitine transport defect 2014-05-28 no assertion criteria provided clinical testing
Natera, Inc. RCV000635351 SCV001462821 likely pathogenic Renal carnitine transport defect 2020-09-16 no assertion criteria provided clinical testing

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