Variant: NM_000152.5(GAA):c.2331+2T>A

CA16041906

371281 (ClinVar)

Gene: GAA

Condition: glycogen storage disease II

Inheritance Mode: Autosomal recessive inheritance

UUID: 7cfcb213-612a-4c23-982e-bfa9e6d58385

Approved on: 2024-12-19

Published on: 2025-02-28

HGVS expressions

NM_000152.5:c.2331+2T>A
NM_000152.5(GAA):c.2331+2T>A
NC_000017.11:g.80117111T>A
CM000679.2:g.80117111T>A
NC_000017.10:g.78090910T>A
CM000679.1:g.78090910T>A
NC_000017.9:g.75705505T>A
NG_009822.1:g.20556T>A
ENST00000570803.6:c.2331+2T>A
ENST00000572080.2:c.*469+2T>A
ENST00000577106.6:c.2331+2T>A
ENST00000302262.8:c.2331+2T>A
ENST00000302262.7:c.2331+2T>A
ENST00000390015.7:c.2331+2T>A
ENST00000573556.1:n.284+2T>A
NM_000152.3:c.2331+2T>A
NM_001079803.1:c.2331+2T>A
NM_001079804.1:c.2331+2T>A
NM_000152.4:c.2331+2T>A
NM_001079803.2:c.2331+2T>A
NM_001079804.2:c.2331+2T>A
NM_001079803.3:c.2331+2T>A
NM_001079804.3:c.2331+2T>A

Pathogenic

• Met criteria codes: PM2_Supporting PVS1 PP4_Moderate PM3

• Not Met criteria codes: PP3

Expert Panel

Lysosomal Diseases VCEP

Criteria Specification Information

Criteria Specification: ClinGen Lysosomal Storage Disorders Variant Curation Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines Version 2

Evidence submitted by expert panel

Lysosomal Diseases VCEP

The NM_000152.5:c.2331+2T>A variant in GAA occurs within the canonical splice donor site of intron 16. RT-PCR of RNA from cultured fibroblasts from a patient who is compound heterozygous for this variant revealed that c.2331+2T>A leads to use of an alternative splice donor at c.2315, resulting in a frameshift, premature stop codon and nonsense-mediated decay in a gene in which loss-of-function is an established disease mechanism (PMID 33168984). Western blot of protein from cultured fibroblasts from another patient with this variant found absence of cross-reactive immunological material for GAA supporting that this variant results in lack of gene product (PMID 22252923)(PVS1). At least 5 patients with Pompe disease have been reported with this variant including 4 patients with documented GAA deficiency (PMID 26693141, 27189384, 32071926)(PP4_Moderate). Of these patients, three are compound heterozygous for the variant and c.-32-13T>G, with one confirmed in trans (PMIDs 27189384, 30922962, 29149851), one is compound heterozygous for the variant and c.1327-61_1437+171del, phase unknown (PMID 32071926), and one patient is homozygous (PMID 26693141)(PM3). The highest population minor allele frequency in gnomAD v2.1.1 is 0.00001 in the European non-Finnish population, which is lower than the ClinGen LD VCEP’s threshold for PM2_Supporting (<0.001), meeting this criterion (PM2_Supporting). The computational splicing predictor SpliceAI gives a score of 0.97 for donor loss, predicting that the variant disrupts the donor splice site of intron 16 of GAA. But since PVS1 is applied, PP3 cannot be applied at the same time. There is a ClinVar entry for this variant (Variation ID: 371281, 2 star review status) with seven submitters classifying the variant as pathogenic. In summary, this variant meets the criteria to be classified as pathogenic for Pompe disease. ACMG/AMP criteria met, as specified by the ClinGen Lysosomal Diseases VCEP (ACMG/AMP specifications version 2.0): PVS1, PM3, PP4_Moderate, PM2_Supporting. (Classification approved by the ClinGen Lysosomal Diseases Variant Curation Expert Panel on December 19, 2024)

Met criteria codes

• PM2_Supporting: The highest population minor allele frequency in gnomAD v2.1.1 is 0.00001 in the European non-Finnish population, which is lower than the ClinGen LSD VCEP’s threshold for PM2_Supporting (<0.001), meeting this criterion (PM2_Supporting).
• PVS1: The NM_000152.5:c.2331+2T>A variant in GAA occurs within the canonical splice donor site of intron 16. RT-PCR of RNA from cultured fibroblasts of a patient compound heterozygous for this variant and a known pathogenic variant in GAA revealed that c.2331+2T>A leads to use of an alternative splice donor at c.2315, which results in a frameshift, the generation of a premature stop codon and mRNA decay in a gene in which loss-of-function is an established disease mechanism (PMID 33168984). Western blot of protein from cultured fibroblasts from a patient with this variant found absence of cross-reactive immunological material for GAA supporting that this variant results in lack of gene product (PMID 22252923)(PVS1).
• PP4_Moderate: At least 4 patients with this variant have been reported with Pompe disease and documented GAA deficiency including 2 patients with <1% of normal GAA activity in fibroblasts (PMID 26693141, 32071926) and 2 patients with GAA activity below the normal range in fibroblasts (PMID 27189384)(PP4_Moderate).
• PM3: At least 5 patients with Pompe disease have been reported with this variant. Of these patients, three are compound heterozygous for the variant and c.-32-13T>G (one confirmed in trans, PMIDs 27189384, 30922962; phase unknown for two, PMIDs 27189384, 30922962, 29149851, 1 point), one is compound heterozygous for the variant and c.1327-61_1437+171del (PMID 32071926), and one patient is homozygous (PMID 26693141, 0.5 points). The in trans data for the patient with c.1327-61_1437+171del will be used in the assessment of that variant and is not included here in order to avoid circular logic. Total points for PM3, 1.5 points (PM3).

Not Met criteria codes

• PP3: The computational splicing predictor SpliceAI gives a score of 0.97 for donor loss, predicting that the variant disrupts the donor splice site of intron 16 of GAA. But since PVS1 is applied, PP3 is not applied.