Submissions for variant NM_000642.3(AGL):c.214_215del (p.Glu72fs)

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Total submissions: 4

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Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Invitae	RCV001210264	SCV001381743	pathogenic	Glycogen storage disease type III	2023-12-14	criteria provided, single submitter	clinical testing	This sequence change creates a premature translational stop signal (p.Glu72Lysfs*4) in the AGL gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in AGL are known to be pathogenic (PMID: 19299494). This variant is present in population databases (rs754978531, gnomAD 0.003%). This variant has not been reported in the literature in individuals affected with AGL-related conditions. ClinVar contains an entry for this variant (Variation ID: 940640). For these reasons, this variant has been classified as Pathogenic.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV001210264	SCV003800830	likely pathogenic	Glycogen storage disease type III	2023-01-31	criteria provided, single submitter	clinical testing	Variant summary: AGL c.214_215delGA (p.Glu72LysfsX4) 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 4e-06 in 251208 control chromosomes (gnomAD). To our knowledge, no occurrence of c.214_215delGA in individuals affected with Glycogen Storage Disease Type III and no experimental evidence demonstrating its impact on protein function have been reported. One ClinVar submitter (evaluation after 2014) cites this variant as pathogenic. Based on the evidence outlined above, the variant was classified as likely pathogenic.
Genome-Nilou Lab	RCV001210264	SCV004049912	likely pathogenic	Glycogen storage disease type III	2023-04-11	criteria provided, single submitter	clinical testing
Baylor Genetics	RCV001210264	SCV004215479	pathogenic	Glycogen storage disease type III	2023-04-06	criteria provided, single submitter	clinical testing

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