Submissions for variant NM_001164277.2(SLC37A4):c.169_175del (p.Ser57fs)

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Total submissions: 4

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Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Labcorp Genetics (formerly Invitae), Labcorp	RCV000806503	SCV000946507	pathogenic	Glucose-6-phosphate transport defect	2021-07-05	criteria provided, single submitter	clinical testing	This sequence change creates a premature translational stop signal (p.Ser57Leufs*16) in the SLC37A4 gene. It is expected to result in an absent or disrupted protein product. This variant is present in population databases (rs782501672, ExAC 0.01%). This variant has not been reported in the literature in individuals with SLC37A4-related disease. Loss-of-function variants in SLC37A4 are known to be pathogenic (PMID: 9758626, 10940311). For these reasons, this variant has been classified as Pathogenic.
Centogene AG - the Rare Disease Company	RCV000806503	SCV001424491	pathogenic	Glucose-6-phosphate transport defect		criteria provided, single submitter	clinical testing
Baylor Genetics	RCV000806503	SCV004202478	pathogenic	Glucose-6-phosphate transport defect	2023-11-19	criteria provided, single submitter	clinical testing
Neuberg Centre For Genomic Medicine, NCGM	RCV000806503	SCV005329286	likely pathogenic	Glucose-6-phosphate transport defect	2023-05-20	criteria provided, single submitter	clinical testing	The observed frameshift variant c.169_175del(p.Ser57LeufsTer16) in SLC37A4 gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The c.169_175del variant has 0.002% allele frequency in gnomAD Exomes. This variant has been submitted to the ClinVar database as Pathogenic. However, study on multiple affected individuals and functional impact of the variant is not available. This variant causes a frameshift starting with codon Serine 57, changes this amino acid to Leucine residue, and creates a premature Stop codon at position 16 of the new reading frame, denoted p.Ser57LeufsTer16. This variant is predicted to cause loss of normal protein function through protein truncation. Loss of function variants have been previously reported to be disease causing (Chen LY, et al., 2000). For these reasons, this variant has been classified as Likely Pathogenic.

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