Submissions for variant NM_000152.5(GAA):c.971C>T (p.Pro324Leu)

gnomAD frequency: 0.00002  dbSNP: rs750030887

Total submissions: 11

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
ClinGen Lysosomal Storage Disorder Variant Curation Expert Panel	RCV000670143	SCV002817445	uncertain significance	Glycogen storage disease, type II	2024-04-02	reviewed by expert panel	curation	The NM_000152.5:c.971C>T variant in GAA is a missense variant predicted to cause substitution of Proline by Leucine at amino acid 324 (p.Pro324Leu). One patient is reported to be compound heterozygous for the variant and c.794G>A (p.Ser265Asn). However the clinical symptoms were not consistent with Pompe disease. Another patient, with history of muscle weakness, had documented GAA deficiency in leukocytes after immunoprecipitation, 15% of normal mean control level, which does not meet the LD VCEP's threshold for PP4. IN addition, the cDNA changes for the variants in this patient was not provided, and therefore this data was not included (PMID:11071489) (PP4 not met). The highest population minor allele frequency in gnomAD v2.1.1 is 0.00004014 (1/24914 alleles) in the African /African American population, which is lower than the ClinGen LSD VCEP’s threshold for PM2_Supporting (<0.001), meeting this criterion. The computational predictor REVEL gives a score of 0.788 which is above the threshold predicting a damaging (>0.7) impact on GAA function (PP3). When expressed in CHO cells, the variant has activity >2% normal but, because further details are not available regarding the activity of the variant, PS3 was not applied. There is a ClinVar entry for this variant (Variant ID: 431990). In summary, the variant meets the criteria to be classified as a variant of uncertain significance for Pompe disease, based on the GAA-specific ACMG/AMP criteria applied, as specified by the ClinGen Lysosomal Storage Disorders Variant Curation Expert panel (specifications version 2.0): PM2_Supporting, PP3. (The classification was first approved by the ClinGen Lysosomal Diseases Variant Curation Expert Panel on Oct. 4th, 2022. The classification was re-evaluated and re-approved on April 2, 2024).
GeneDx	RCV000498314	SCV000589627	likely pathogenic	not provided	2020-09-02	criteria provided, single submitter	clinical testing	Functional studies found that P324L is associated with reduced acid alpha-glucosidase compared to wild-type (Flanagan et al., 2009); Not observed at a significant frequency in large population cohorts (Lek et al., 2016); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This variant is associated with the following publications: (PMID: 11071489, 19862843)
Counsyl	RCV000670143	SCV000794962	uncertain significance	Glycogen storage disease, type II	2017-10-24	criteria provided, single submitter	clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000670143	SCV000919373	likely pathogenic	Glycogen storage disease, type II	2017-10-30	criteria provided, single submitter	clinical testing	Variant summary: The GAA c.971C>T (p.Pro324Leu) variant involves the alteration of a conserved nucleotide. 5/5 in silico tools predict a damaging outcome for this variant. This variant was found in 2/246128 control chromosomes at a frequency of 0.0000081, which does not exceed the estimated maximal expected allele frequency of a pathogenic GAA variant (0.0042205). The variant was reported in a patient with severe infantile form of Pompe disease who carried a second second GAA mutation (W490X) and had 15% residual GAA activity (Laforet_2000). Additionally, a functional study performed in COS-7 cells showed the variant to have reduced GAA activity and GAA protein compared to wild-type (Flanagan_2009). In addition, one clinical diagnostic laboratory classified this variant as likely pathogenic. Taken together, this variant is classified as likely pathogenic.
Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard	RCV000670143	SCV001422623	uncertain significance	Glycogen storage disease, type II	2020-01-22	criteria provided, single submitter	curation	The heterozygous p.Pro324Leu variant in GAA has been reported in 1 French individual with Glycogen Storage Disease II (PMID: 11071489), and has also been reported as a likely pathogenic variant by GeneDx and Integrated Genetics, and a VUS by Counsyl in ClinVar (Variation ID: 431990). This variant has been identified in 0.004% (1/24914) of African chromosomes, 0.003% (1/30616) of South Asian chromosomes and 0.0007754% (1/128970) of European (non-Finnish) chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs750030887). 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 with COS cells transfected with this variant provide some evidence that the p.Pro324Leu variant may impact GAA processing based on Western Blots (PMID: 19862843). However, these types of assays may not accurately represent biological function. Computational prediction tools and conservation analyses suggest that this variant may impact the protein, though this information is not predictive enough to determine pathogenicity. This variant was reported in combination with a rare nonsense variant and in an individual with Glycogen Storage Disease II (PMID: 11071489). In summary, while there is some suspicion for a pathogenic role, the clinical significance of this variant is uncertain. ACMG/AMP Criteria applied: PM2, PP3 (Richards 2015).
Genome-Nilou Lab	RCV000670143	SCV001810562	likely pathogenic	Glycogen storage disease, type II	2021-07-22	criteria provided, single submitter	clinical testing
Suma Genomics	RCV000670143	SCV001837640	uncertain significance	Glycogen storage disease, type II		criteria provided, single submitter	clinical testing
Revvity Omics, Revvity	RCV000498314	SCV002025197	likely pathogenic	not provided	2023-06-06	criteria provided, single submitter	clinical testing
Labcorp Genetics (formerly Invitae), Labcorp	RCV000670143	SCV003284669	uncertain significance	Glycogen storage disease, type II	2022-08-05	criteria provided, single submitter	clinical testing	This sequence change replaces proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 324 of the GAA protein (p.Pro324Leu). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This missense change has been observed in individual(s) with clinical features of GAA-related conditions (PMID: 11071489, 34864681). ClinVar contains an entry for this variant (Variation ID: 431990). 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. Experimental studies are conflicting or provide insufficient evidence to determine the effect of this variant on GAA function (PMID: 19862843). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Baylor Genetics	RCV000670143	SCV004195453	likely pathogenic	Glycogen storage disease, type II	2023-10-11	criteria provided, single submitter	clinical testing
Natera, Inc.	RCV000670143	SCV001455598	likely pathogenic	Glycogen storage disease, type II	2020-09-16	no assertion criteria provided	clinical testing