Submissions for variant NM_000152.5(GAA):c.2236T>C (p.Trp746Arg)

dbSNP: rs1479740763

Total submissions: 8

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Eurofins Ntd Llc (ga)	RCV000726989	SCV000704721	likely pathogenic	not provided	2017-01-13	criteria provided, single submitter	clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000598534	SCV001554637	pathogenic	Glycogen storage disease, type II	2023-07-28	criteria provided, single submitter	clinical testing	Variant summary: GAA c.2236T>C (p.Trp746Arg) results in a non-conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. This alters a highly conserved residue (HGMD) in which other missense variants have been found in association with disease and some have been classified as pathogenic by ClinVar submitters (e.g. p.Trp746Cys). The variant was absent in 250780 control chromosomes (gnomAD). c.2236T>C has been reported in the literature in individuals affected with Glycogen Storage Disease, Type 2 (Pompe Disease; Nino_2013, Mori_2017, Nallamilli_2018, Kishnani_2019), and some were reported as compound heterozygous with a pathogenic variant. These data indicate that the variant is likely to be associated with disease. At least one publication reports experimental evidence evaluating an impact on protein function (Nino_2013), finding that the variant results in <10% of normal GAA activity. The following publications have been ascertained in the context of this evaluation (PMID: 29122469, 23430493, 30564623, 31086307, 31254424, 33202836). Six submitters have cited clinical-significance assessments for this variant to ClinVar after 2014, and classified it as pathogenic/likely pathogenic (n=5) or uncertain significance (n=1). Based on the evidence outlined above, the variant was classified as pathogenic.
GeneDx	RCV000726989	SCV001793120	pathogenic	not provided	2020-06-09	criteria provided, single submitter	clinical testing	Published functional studies in HEK293 cells demonstrate a significant decrease or loss of enzyme activity compared to controls (Nino et al., 2013); Not observed in large population cohorts (Lek et al., 2016); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 31086307, 32064362, 21637107, 29122469, 23430493, 31342611, 30564623)
Genome-Nilou Lab	RCV000598534	SCV001810183	likely pathogenic	Glycogen storage disease, type II	2021-07-22	criteria provided, single submitter	clinical testing
Revvity Omics, Revvity	RCV000726989	SCV002023794	pathogenic	not provided	2022-04-14	criteria provided, single submitter	clinical testing
Labcorp Genetics (formerly Invitae), Labcorp	RCV000598534	SCV002235074	pathogenic	Glycogen storage disease, type II	2024-02-11	criteria provided, single submitter	clinical testing	This sequence change replaces tryptophan, which is neutral and slightly polar, with arginine, which is basic and polar, at codon 746 of the GAA protein (p.Trp746Arg). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with GAA-related conditions (PMID: 23430493, 29122469). ClinVar contains an entry for this variant (Variation ID: 499293). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt GAA protein function with a positive predictive value of 95%. Experimental studies have shown that this missense change affects GAA function (PMID: 23430493). This variant disrupts the p.Trp746 amino acid residue in GAA. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 9535769, 21232767, 21757382, 25093132, 27099502). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic.
Baylor Genetics	RCV000598534	SCV004197813	likely pathogenic	Glycogen storage disease, type II	2023-06-19	criteria provided, single submitter	clinical testing
Counsyl	RCV000598534	SCV000800152	uncertain significance	Glycogen storage disease, type II	2018-05-23	flagged submission	clinical testing