ClinVar Miner

Submissions for variant NM_003060.4(SLC22A5):c.453G>A (p.Val151=)

gnomAD frequency: 0.00003  dbSNP: rs386134194
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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 RCV000022323 SCV000829524 pathogenic Renal carnitine transport defect 2025-01-30 criteria provided, single submitter clinical testing This sequence change affects codon 151 of the SLC22A5 mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the SLC22A5 protein. This variant is present in population databases (rs386134194, gnomAD 0.009%). This variant has been observed in individual(s) with primary carnitine deficiency (PMID: 28841266; internal data). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 25375). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.
Mendelics RCV000022323 SCV001136972 pathogenic Renal carnitine transport defect 2023-03-24 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV000022323 SCV002055747 uncertain significance Renal carnitine transport defect 2021-07-15 criteria provided, single submitter clinical testing
Baylor Genetics RCV000022323 SCV004201252 likely pathogenic Renal carnitine transport defect 2024-02-29 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV000022323 SCV005669197 likely pathogenic Renal carnitine transport defect 2024-04-16 criteria provided, single submitter clinical testing
Clinical Genomics Laboratory, Stanford Medicine RCV000022323 SCV001427024 uncertain significance Renal carnitine transport defect 2019-01-10 no assertion criteria provided clinical testing The p.Val151= variant in the SLC22A5 gene has been seen previously in 3 individuals with primary systemic carnitine deficiency (unpublished, ARUP Primary Carnitine Deficiency and SLC22A5 Database). In two of these patients, a second likely pathogenic/pathogenic variant was identified [Thr440Met; Pro46Ser], consistent with autosomal recessive inheritence. The p.Val151= variant has been identified in 11/129200 non-Finnish European alleles by the Genome Aggregation Database (http://gnomad.broadinstitute.org/). Computational splicing tools predict formation of a cryptic splice site; however, the accuracy of in silico algorithms is limited. These data were assessed using the ACMG/AMP variant interpretation guidelines. In summary, the significance of the p.Val151= variant is uncertain. However, there is suspicion that this variant could be associated with primary systemic carnitine deficiency as it has been seen in 3 other affected individuals. Additional information is needed to resolve the significance of this variant. [ACMG evidence codes used: PM2, PM3, PP3]

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