ClinVar Miner

Submissions for variant NM_000387.6(SLC25A20):c.84del (p.His29fs)

gnomAD frequency: 0.00001  dbSNP: rs587776760
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000186166 SCV000239192 pathogenic not provided 2014-01-16 criteria provided, single submitter clinical testing The c.84delT mutation in the SLC25A20 gene has been reported previously in association with carnitine-acylcarnitine translocase (CACT) deficiency using alternate nomenclature (Ogawa et al., 2000). The deletion causes a frameshift starting with codon Histidine 29, changes this amino acid to a Threonine residue and creates a premature Stop codon at position 100 of the new reading frame, denoted p.His29ThrfsX100. This mutation is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The variant is found in SLC25A20 panel(s).
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000012919 SCV002570586 pathogenic Carnitine acylcarnitine translocase deficiency 2022-07-29 criteria provided, single submitter clinical testing Variant summary: SLC25A20 c.84delT (p.His29ThrfsX100) 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. The variant allele was found at a frequency of 4.2e-06 in 236062 control chromosomes (gnomAD). c.84delT has been reported in the literature in individuals affected with Carnitine-Acylcarnitine Translocase Deficiency (e.g. Ogawa_2000, Hsu_2001). These data indicate that the variant is likely to be associated with disease. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as pathogenic.
Labcorp Genetics (formerly Invitae), Labcorp RCV000012919 SCV004281696 pathogenic Carnitine acylcarnitine translocase deficiency 2023-10-08 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.His29Thrfs*100) in the SLC25A20 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in SLC25A20 are known to be pathogenic (PMID: 25614308). This variant is present in population databases (rs587776760, gnomAD 0.002%). This premature translational stop signal has been observed in individual(s) with carnitine-acylcarnitine translocase deficiency (PMID: 10697964, 11592821). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. This variant is also known as 120delT and 146delT. ClinVar contains an entry for this variant (Variation ID: 12136). For these reasons, this variant has been classified as Pathogenic.
OMIM RCV000012919 SCV000033160 pathogenic Carnitine acylcarnitine translocase deficiency 2000-01-01 no assertion criteria provided literature only

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