Evidence Repository - Clinical Genome Resources

The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]

Variant: NM_000152.5(GAA):c.1099del (p.Trp367fs)

Curation Version - 1.0
Curation History
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CA16041888

370810 (ClinVar)

Gene: GAA

Condition: glycogen storage disease II

Inheritance Mode: Autosomal recessive inheritance

Link to MONDO

UUID: 736d1a81-75c6-48d7-aacf-00c0535e37af

Approved on: 2020-11-02

Published on: 2020-11-12

HGVS expressions

NM_000152.5:c.1099del

NM_000152.5(GAA):c.1099del (p.Trp367fs)

NC_000017.11:g.80108512del

CM000679.2:g.80108512del

NC_000017.10:g.78082311del

CM000679.1:g.78082311del

NC_000017.9:g.75696906del

NG_009822.1:g.11957del

ENST00000570803.6:c.1099del

ENST00000572080.2:c.1099del

ENST00000577106.6:c.1099del

ENST00000302262.8:c.1099del

ENST00000302262.7:c.1099del

ENST00000390015.7:c.1099del

NM_000152.3:c.1099del

NM_001079803.1:c.1099del

NM_001079804.1:c.1099del

NM_000152.4:c.1099del

NM_001079803.2:c.1099del

NM_001079804.2:c.1099del

NM_001079803.3:c.1099del

NM_001079804.3:c.1099del

Likely Pathogenic

PM2 PVS1

Evidence Links 0

Expert Panel

Lysosomal Diseases VCEP

Criteria Specification Information

Criteria Specifications for this VCEP

Evidence submitted by expert panel

Lysosomal Diseases VCEP

This variant, c.1099del (p.Trp367GlyfsTer25), is a frameshift variant that is predicted to result in a premature termination codon, nonsense mediated decay, and lack of gene product, meeting PVS1. This variant is not in gnomAD v2.1.1, meeting PM2. To our knowledge, this variant has not been reported in a patient with Pompe disease in the literature, and results of functional studies are not available. There is a ClinVar entry for this variant (Variation ID: 370810, 1 star review status) with one submitter classifying the variant as likely pathogenic. In summary, this variant meets the criteria to be classified as likely pathogenic for Pompe disease. GAA-specific ACMG/AMP criteria applied, as specified by the ClinGen LSD VCEP: PVS1, PM2.

PM2

This variant is not in gnomAD v2.1.1.

PVS1

This is a frameshift variant which is predicted to result in a premature termination codon, nonsense mediated decay, and lack of gene product. Therefore, PVS1 can be applied.

Curation History

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