Submissions for variant NM_000152.5(GAA):c.781G>A (p.Ala261Thr)

gnomAD frequency: 0.00004  dbSNP: rs543360994

Total submissions: 6

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
ClinGen Lysosomal Storage Disorder Variant Curation Expert Panel	RCV000536776	SCV002817448	uncertain significance	Glycogen storage disease, type II	2022-11-01	reviewed by expert panel	curation	The NM_000152.5:c.781G>A variant in GAA is a missense variant predicted to cause substitution of Ala by Thr at amino acid 261 (p.Ala261Thr). One patient with infantile-onset Pompe disease who was homozygous for this variant has been reported;, the parents were confirmed to be heterozygous (PMID 31510962) (PM3_Supporting). The patients symptoms included dyspnea, poor feeding, failure to thrive, delayed motor milestone, short PR interval, biventricular hypertrophy, and severe intellectual disability. GAA activity was 0.43% of normal (PMID 31510962)(PP4_Moderate). The highest population minor allele frequency in gnomAD v2.1.1 is 0.00010 (3/30616 alleles) in the South Asian population, which is lower than the ClinGen LSD VCEP’s threshold for PM2_Supporting (<0.001), meeting this criterion (PM2_Supporting). When expressed in COS cells, the variant results in reduced GAA activity (66% in cell extract and 5% in culture medium comparing to wildtype) and is classified as class D for the severity rating (PMID 31510962) (BS3_Supporting). The computational predictor REVEL gives a score of 0.584 which is neither above nor below the thresholds predicting a damaging (>0.7) or benign (<0.5) impact on GAA function. The computational splicing predictor SpliceAI predicts no impact on splicing. Two different missense variants, c.781G>C (p.Ala261Pro) and c.782C>T (p.Ala261Val) in the same codon have been reported in patients with Pompe disease. However, these variants have not yet met the criteria to be classified as pathogenic or likely pathogenic by the ClinGen LSD VCEP (PM5 not met). There is a ClinVar entry for this variant (Variation ID: 456438). In summary, this variant meets the criteria to be classified as Uncertain significance for Pompe disease based on the ACMG/AMP criteria applied, as specified by the ClinGen Lysosomal Storage Disorders Variant Curation Expert panel (Specification Version 2.0): PM2_supporting, PM3_supporting, PP4_Moderate, BS3_supporting. (Classification approved by the ClinGen LSD VCEP on Nov 1, 2022).
Labcorp Genetics (formerly Invitae), Labcorp	RCV000536776	SCV000626640	likely pathogenic	Glycogen storage disease, type II	2023-12-16	criteria provided, single submitter	clinical testing	This sequence change replaces alanine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 261 of the GAA protein (p.Ala261Thr). This variant is present in population databases (rs543360994, gnomAD 0.01%). This missense change has been observed in individual(s) with Pompe disease (PMID: 31510962). ClinVar contains an entry for this variant (Variation ID: 456438). 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) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on GAA protein function. Experimental studies have shown that this missense change affects GAA function (PMID: 31510962). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.
Fulgent Genetics, Fulgent Genetics	RCV000536776	SCV002789340	uncertain significance	Glycogen storage disease, type II	2021-11-24	criteria provided, single submitter	clinical testing
Revvity Omics, Revvity	RCV003144319	SCV003828509	uncertain significance	not provided	2022-11-01	criteria provided, single submitter	clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV003235274	SCV003934319	uncertain significance	not specified	2023-05-19	criteria provided, single submitter	clinical testing	Variant summary: GAA c.781G>A (p.Ala261Thr) results in a non-conservative amino acid change located in the Glycoside hydrolase family 31, N-terminal domain (IPR025887) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 2e-05 in 251028 control chromosomes (gnomAD). c.781G>A has been reported in the literature in a homozygous individual affected with infantile Glycogen Storage Disease (Pompe Disease) (example: Ngiwsara_2019). These data indicate that the variant may be associated with disease. The following publications have been ascertained in the context of this evaluation (PMID: 31510962, 16865695). Five clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 and classified the variant as VUS (n=3) and pathogenic/likely pathogenic (n=2). Based on the evidence outlined above, the variant was classified as VUS-possibly pathogenic.
Department of Pediatrics, Division of Medical Genetics, Faculty of Medicine Ramathibodi Hospital, Mahidol University	RCV000536776	SCV000925965	pathogenic	Glycogen storage disease, type II	2019-07-10	no assertion criteria provided	research	The c.781G>A (p.A261T) is present in population database (rs543360994, ExAC 0.00002%). This variant has not been reported in the literature in individuals with GAA-related disease. ClinVar contains an entry for this variant (Variation ID: 456438). It was reported to have uncertain impact on protein function and there is no indication that it causes disease. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, Polyphen-2, PredictSNP2, CADD, DANN, FATHMM, and FunSeq2) all suggest that this variant is damaging/deleterious. Our study provided evident supported the impact of amino acid substitution at this position on GAA function. In vitro expression analysis of c.781G>A (p.A261T) indicates that this variant yielded partial reduction of enzyme activity and impaired GAA processing and transportation. We interpret c.781G>A (p.A261T) as a pathogenic variant.