ClinVar Miner

Submissions for variant NM_003060.4(SLC22A5):c.806del (p.Leu269fs)

gnomAD frequency: 0.00001  dbSNP: rs386134204
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000299145 SCV000329850 pathogenic not provided 2020-08-31 criteria provided, single submitter clinical testing Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Not observed at a significant frequency in large population cohorts (Lek et al., 2016); This variant is associated with the following publications: (PMID: 26828774, 23379544, 12409266, 20574985, 16602102)
Counsyl RCV000022345 SCV000485830 likely pathogenic Renal carnitine transport defect 2016-02-19 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000022345 SCV000756762 pathogenic Renal carnitine transport defect 2024-11-14 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Leu269Hisfs*27) in the SLC22A5 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in SLC22A5 are known to be pathogenic (PMID: 9916797). This variant is present in population databases (rs386134204, gnomAD 0.003%). This premature translational stop signal has been observed in individual(s) with primary carnitine deficiency (PMID: 12409266, 23379544). ClinVar contains an entry for this variant (Variation ID: 25392). For these reasons, this variant has been classified as Pathogenic.
Genome-Nilou Lab RCV000022345 SCV002055814 pathogenic Renal carnitine transport defect 2021-07-15 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000022345 SCV002548262 pathogenic Renal carnitine transport defect 2022-05-26 criteria provided, single submitter clinical testing Variant summary: SLC22A5 c.806delT (p.Leu269HisfsX27) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. Truncations downstream of this position have been classified as pathogenic by our laboratory. At least one publication reports experimental evidence that this variant affects mRNA splicing. The variant allele was found at a frequency of 8e-06 in 251418 control chromosomes. c.806delT has been reported in the literature in individuals affected with Systemic Primary Carnitine Deficiency. These data indicate that the variant may be associated with disease. Four clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.
Baylor Genetics RCV000022345 SCV004201255 pathogenic Renal carnitine transport defect 2024-03-28 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV000022345 SCV005669216 pathogenic Renal carnitine transport defect 2024-05-14 criteria provided, single submitter clinical testing

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