ClinVar Miner

Submissions for variant NM_001164277.1(SLC37A4):c.344_345dup (p.Leu116fs) (rs782604758)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000665873 SCV000790065 likely pathogenic Glucose-6-phosphate transport defect 2017-03-03 criteria provided, single submitter clinical testing
Invitae RCV000665873 SCV001388923 pathogenic Glucose-6-phosphate transport defect 2019-05-10 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Leu116Glyfs*31) in the SLC37A4 gene. It is expected to result in an absent or disrupted protein product. This variant is present in population databases (rs782604758, ExAC 0.003%). This variant has been observed in an individual affected with glycogen storage disease (PMID: 10518030). ClinVar contains an entry for this variant (Variation ID: 550962). Loss-of-function variants in SLC37A4 are known to be pathogenic (PMID: 9758626, 10940311). For these reasons, this variant has been classified as Pathogenic.
Integrated Genetics/Laboratory Corporation of America RCV000665873 SCV001432012 pathogenic Glucose-6-phosphate transport defect 2020-08-21 criteria provided, single submitter clinical testing Variant summary: SLC37A4 c.344_345dupGG (p.Leu116GlyfsX31) 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 4.3e-06 in 233828 control chromosomes. c.344_345dupGG has been reported in the literature in multiple individuals affected with Glycogen Storage Disease Type Ib (examples- Galli_1999, Sperb-Ludwig_2019). These data indicate that the variant is very likely to be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Two clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. Both laboratories classified the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.

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