The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
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Variant: NM_000152.5(GAA):c.2617dup (p.Tyr873fs)

CA658824790

550478 (ClinVar)

Gene: GAA
Condition: glycogen storage disease II
Inheritance Mode: Autosomal recessive inheritance
UUID: 300443cc-c894-4008-9935-4babb82a4986
Approved on: 2024-04-05
Published on: 2024-04-05

HGVS expressions

NM_000152.5:c.2617dup
NM_000152.5(GAA):c.2617dup (p.Tyr873fs)
NC_000017.11:g.80118328dup
CM000679.2:g.80118328dup
NC_000017.10:g.78092127dup
CM000679.1:g.78092127dup
NC_000017.9:g.75706722dup
NG_009822.1:g.21773dup
ENST00000570803.6:c.2617dup
ENST00000572080.2:c.*755dup
ENST00000577106.6:c.2617dup
ENST00000302262.8:c.2617dup
ENST00000302262.7:c.2617dup
ENST00000390015.7:c.2617dup
ENST00000573556.1:n.570dup
NM_000152.3:c.2617dup
NM_001079803.1:c.2617dup
NM_001079804.1:c.2617dup
NM_000152.4:c.2617dup
NM_001079803.2:c.2617dup
NM_001079804.2:c.2617dup
NM_001079803.3:c.2617dup
NM_001079804.3:c.2617dup

Likely Pathogenic

Met criteria codes 2
PVS1 PM2_Supporting

Evidence Links 0

Expert Panel

Criteria Specification Information

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

PDF
Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Lysosomal Diseases VCEP
The NM_000152.5:c.2617dup (p.Tyr873LeufsTer11) variant in GAA is a frameshift variant that is predicted to cause a premature stop codon at the junction of biologically-relevant-exons 18 and 19 (GAA has 20 exons), leading to nonsense mediated decay in a gene in which loss-of-function is an established disease mechanism (PVS1). This variant is absent in gnomAD v2.1.1 (PM2_Supporting). To our knowledge, this variant has not been reported in the literature in patients with Pompe disease. There is a ClinVar entry for this variant (Variation ID: 550478). The classification of this variant has been upgraded from Variant of Uncertain Significance to likely pathogenic based on the recommendations of the ClinGen Sequence Variant Interpretation Working Group, that a variant meeting PVS1 and PM2_Supporting is classified as Likely Pathogenic (https://clinicalgenome.org/site/assets/files/5182/pm2_-_svi_recommendation_-_approved_sept2020.pdf ). The classification was first approved by the ClinGen Lysosomal Diseases Variant Curation Expert Panel on September 7, 2021. Since then, the data for this variant have been re-evaluated - no new data were identified. The classification of likely pathogenic was reapproved on April 5, 2024. GAA-specific ACMG/AMP criteria met, as specified by the ClinGen Lysosomal Diseases Variant Curation Expert Panel (Specifications Version 2.0): PVS1, PM2_Supporting.
Met criteria codes
PVS1
The NM_000152.5:c.2617dup (p.Tyr873LeufsTer11) variant in GAA is a frameshift variant that is predicted to cause a premature stop codon at the junction of biologically-relevant-exons 18 and 19 (GAA has 20 exons), leading to nonsense mediated decay in a gene in which loss-of-function is an established disease mechanism (PVS1).
PM2_Supporting
This variant is absent in gnomAD v2.1.1 (PM2_Supporting).
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