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Variant: NM_000152.5(GAA):c.471del (p.Thr158fs)

CA16041883

371501 (ClinVar)

Gene: GAA
Condition: glycogen storage disease II
Inheritance Mode: Autosomal recessive inheritance
UUID: ed7c0f06-6f0f-4e76-847b-7067e361ae4c
Approved on: 2020-07-21
Published on: 2020-11-11

HGVS expressions

NM_000152.5:c.471del
NM_000152.5(GAA):c.471del (p.Thr158fs)
NC_000017.11:g.80105057del
CM000679.2:g.80105057del
NC_000017.10:g.78078856del
CM000679.1:g.78078856del
NC_000017.9:g.75693451del
NG_009822.1:g.8502del
ENST00000570803.6:c.471del
ENST00000572080.2:c.471del
ENST00000577106.6:c.471del
ENST00000302262.8:c.471del
ENST00000302262.7:c.471del
ENST00000390015.7:c.471del
ENST00000570803.5:c.471del
ENST00000577106.5:c.471del
NM_000152.3:c.471del
NM_001079803.1:c.471del
NM_001079804.1:c.471del
NM_000152.4:c.471del
NM_001079803.2:c.471del
NM_001079804.2:c.471del
NM_001079803.3:c.471del
NM_001079804.3:c.471del
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Likely Pathogenic

Met criteria codes 2
PM2 PVS1

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Lysosomal Diseases VCEP
This variant, c.471del (p.Thr158ProfsTer8), 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: 371501, 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.
Met criteria codes
PM2
This variant is absent 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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