ClinVar Miner

Submissions for variant NM_003060.4(SLC22A5):c.458_459del (p.Val153fs)

dbSNP: rs386134195
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Total submissions: 10
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000186159 SCV000239185 pathogenic not provided 2024-03-05 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 significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 23379544, 26828774, 15714519, 34178604)
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000022324 SCV000698151 pathogenic Renal carnitine transport defect 2017-05-01 criteria provided, single submitter clinical testing Variant summary: The SLC22A5 c.458_459delTG (p.Val153Alafs) variant results in a premature termination codon, predicted to cause a truncated or absent SLC22A5 protein due to nonsense mediated decay, which are commonly known mechanisms for disease. A truncation downstream of this position, c.760C>T (p.Arg254X), has been classified as pathogenic by our laboratory. This variant is absent in 121412 control chromosomes. The variant of interest has been reported in multiple compound heterozygous affected individual via a publication (Dobrowolski_2005) and a database (ARUP). In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as "likely pathogenic/pathogenic." Taken together, this variant has been classified as pathogenic.
Eurofins Ntd Llc (ga) RCV000186159 SCV000704164 pathogenic not provided 2016-12-06 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000022324 SCV000937220 pathogenic Renal carnitine transport defect 2025-01-29 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Val153Alafs*41) 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 (rs386134195, gnomAD 0.004%). This premature translational stop signal has been observed in individual(s) with primary carnitine deficiency (PMID: 15714519). ClinVar contains an entry for this variant (Variation ID: 25376). For these reasons, this variant has been classified as Pathogenic.
CeGaT Center for Human Genetics Tuebingen RCV000186159 SCV001247711 pathogenic not provided 2018-12-01 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV000022324 SCV002055804 pathogenic Renal carnitine transport defect 2021-07-15 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV000022324 SCV002813735 pathogenic Renal carnitine transport defect 2024-05-10 criteria provided, single submitter clinical testing
Baylor Genetics RCV000022324 SCV004201274 pathogenic Renal carnitine transport defect 2024-03-26 criteria provided, single submitter clinical testing
Counsyl RCV000022324 SCV000220438 pathogenic Renal carnitine transport defect 2018-02-26 no assertion criteria provided clinical testing
Natera, Inc. RCV000022324 SCV001462803 pathogenic Renal carnitine transport defect 2020-09-16 no assertion criteria provided clinical testing

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