Submissions for variant NM_000152.5(GAA):c.2432del (p.Leu811fs)

Total submissions: 2

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Invitae	RCV001208130	SCV001379505	pathogenic	Glycogen storage disease, type II	2019-08-03	criteria provided, single submitter	clinical testing	This sequence change creates a premature translational stop signal (p.Leu811Argfs*37) in the GAA gene. It is expected to result in an absent or disrupted protein product. This variant is present in population databases (rs766560578, ExAC 0.002%). This variant has been observed in individual(s) with glycogen storage disease type II (PMID: 16433701, 18429042, 24269976). In at least one individual the data is consistent with the variant being in trans (on the opposite chromosome) from a pathogenic variant. Loss-of-function variants in GAA are known to be pathogenic (PMID: 18425781, 22252923). For these reasons, this variant has been classified as Pathogenic.
Broad Institute Rare Disease Group, Broad Institute	RCV001208130	SCV001422737	pathogenic	Glycogen storage disease, type II	2020-01-22	no assertion criteria provided	curation	The p.Leu811ArgfsTer37 variant in GAA has been reported in at least 5 individuals with glycogen storage disease, segregated with disease in 2 affected relatives from 1 family (PMID: 25763511, 24269976, 16433701, 22252923, 18429042), and has been identified in 0.010% (1/9914) of Ashkenazi Jewish chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs766560578). Although this variant has been seen in the general population, its frequency is low enough to be consistent with a recessive carrier frequency. In vitro functional studies have showed patients with the variant to be CRIM-negative (PMID: 25763511, 22252923). However, these types of assays may not accurately represent biological function. This variant is predicted to cause a frameshift, which alters the protein's amino acid sequence beginning at position 811 and leads to a premature termination codon 37 amino acids downstream. This alteration is then predicted to lead to a truncated or absent protein. Loss of function of the GAA gene is an established disease mechanism in autosomal recessive glycogen storage disease. The phenotype of an individual homozygous for this variant is highly specific for glycogen storage disease based on null GAA enzyme activity in lymphocytes, consistent with disease (PMID: 16433701). Additionally, the presence of this variant in combination with the reported pathogenic variant (p.Asp404Asn) and in an individual with glycogen storage disease increases the likelihood that the p.Leu811ArgfsTer37 variant is pathogenic (PMID: 22538254, 29122469, 29205646, 25687635, 22658377, 23787031, 26497565, 16433701, 243843240). In summary, this variant meets criteria to be classified as pathogenic for glycogen storage disease in an autosomal recessive manner based on the prediction that it causes loss of function, and its presence in combination with another pathogenic variant in an affected individual. ACMG/AMP Criteria applied: PVS1, PM3, PM2, PP4 (Richards 2015).