ClinVar Miner

Submissions for variant NM_003060.4(SLC22A5):c.393+1G>A

dbSNP: rs1057517069
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000409176 SCV000486699 likely pathogenic Renal carnitine transport defect 2016-07-20 criteria provided, single submitter clinical testing
Invitae RCV000409176 SCV001386727 pathogenic Renal carnitine transport defect 2019-05-28 criteria provided, single submitter clinical testing This sequence change affects a donor splice site in intron 1 of the SLC22A5 gene. It is expected to disrupt RNA splicing and likely results in an absent or disrupted protein product. For these reasons, this variant has been classified as Pathogenic. Donor and acceptor splice site variants typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in SLC22A5 are known to be pathogenic (PMID: 9916797). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site, but this prediction has not been confirmed by published transcriptional studies. This variant has been observed in an individual with primary carnitine deficiency (Invitae). In at least one individual the data is consistent with the variant being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 371182). This variant is not present in population databases (ExAC no frequency).
Genome-Nilou Lab RCV000409176 SCV002055799 pathogenic Renal carnitine transport defect 2021-07-15 criteria provided, single submitter clinical testing

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