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NM_000152.5(GAA):c.2269C>T (p.Gln757Ter)

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Interpretation:
Pathogenic​

Review status:
reviewed by expert panel FDA Recognized Database
Submissions:
6 (Most recent: Nov 19, 2021)
Last evaluated:
May 5, 2020
Accession:
VCV000429727.6
Variation ID:
429727
Description:
single nucleotide variant
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NM_000152.5(GAA):c.2269C>T (p.Gln757Ter)

Allele ID
422208
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
17q25.3
Genomic location
17: 78090846 (GRCh37) GRCh37 UCSC
17: 80117047 (GRCh38) GRCh38 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_673t1:c.2269C>T
LRG_673:g.20492C>T
NC_000017.10:g.78090846C>T
... more HGVS
Protein change
Q757*
Other names
-
Canonical SPDI
NC_000017.11:80117046:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA294856548
dbSNP: rs200483245
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 4 reviewed by expert panel May 5, 2020 RCV000664955.4
Pathogenic 2 criteria provided, single submitter Sep 3, 2015 RCV000493446.2
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
GAA - - GRCh38
GRCh37
1548 1588

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(May 05, 2020)
reviewed by expert panel
Method: curation
Glycogen storage disease, type II
(Autosomal recessive inheritance)
Allele origin: germline
ClinGen Lysosomal Storage Disorder Variant Curation Expert Panel, ClinGen
FDA Recognized Database
Accession: SCV001371730.1
Submitted: (May 29, 2020)
Evidence details
Publications
PubMed (2)
Other databases
https://erepo.clinicalgenome.org…
Comment:
This variant, c.2269C>T (p.Gln757Ter), which results in a premature termination codon, is expected to undergo nonsense medicated decay resulting in absence of gene product, meeting … (more)
Pathogenic
(Jan 03, 2017)
criteria provided, single submitter
Method: clinical testing
Glycogen storage disease, type II
Allele origin: unknown
Counsyl
Accession: SCV000788999.1
Submitted: (Jul 10, 2018)
Evidence details
Publications
PubMed (3)
Pathogenic
(Sep 03, 2015)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000582366.3
Submitted: (Jan 29, 2019)
Evidence details
Comment:
The Q757X nonsense pathogenic variant in the GAA gene has been reported previously in a patient with adult-onsetGSDII, who also harbored the common c.-32-13 T>G … (more)
Pathogenic
(Jun 01, 2020)
criteria provided, single submitter
Method: clinical testing
Glycogen storage disease, type II
Allele origin: germline
Invitae
Accession: SCV001589424.1
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (4)
Comment:
This sequence change creates a premature translational stop signal (p.Gln757*) in the GAA gene. It is expected to result in an absent or disrupted protein … (more)
Pathogenic
(Jan 22, 2020)
no assertion criteria provided
Method: curation
Glycogen storage disease, type II
(Autosomal recessive inheritance)
Allele origin: germline
Broad Institute Rare Disease Group, Broad Institute
Accession: SCV001422609.1
Submitted: (Mar 09, 2020)
Evidence details
Publications
PubMed (3)
Other databases
https://erepo.clinicalgenome.org…
Comment:
The p.Gln757Ter variant in GAA has been reported in 1 Serbian, 1 Croatian, and 1 Canadian individuals with Glycogen Storage Disease II (PMID: 29149851, 24337590, … (more)
Pathogenic
(Jan 23, 2020)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
PerkinElmer Genomics
Accession: SCV002023816.1
Submitted: (Nov 19, 2021)
Evidence details

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Identification of GAA variants through whole exome sequencing targeted to a cohort of 606 patients with unexplained limb-girdle muscle weakness. Johnson K Orphanet journal of rare diseases 2017 PMID: 29149851
Effects of immune modulation therapy in the first Croatian infant diagnosed with Pompe disease: a 3-year follow-up study. Markic J Wiener klinische Wochenschrift 2014 PMID: 24337590
Predicting cross-reactive immunological material (CRIM) status in Pompe disease using GAA mutations: lessons learned from 10 years of clinical laboratory testing experience. Bali DS American journal of medical genetics. Part C, Seminars in medical genetics 2012 PMID: 22252923
Update of the Pompe disease mutation database with 107 sequence variants and a format for severity rating. Kroos M Human mutation 2008 PMID: 18425781
Development of a clinical assay for detection of GAA mutations and characterization of the GAA mutation spectrum in a Canadian cohort of individuals with glycogen storage disease, type II. McCready ME Molecular genetics and metabolism 2007 PMID: 17723315
https://erepo.clinicalgenome.org/evrepo/ui/interpretation/224d9d16-4871-4ebc-b18a-c06d9fdc1cec - - - -
https://erepo.clinicalgenome.org/evrepo/ui/interpretation/b0971d5d-fc3b-4e12-bca3-0beb81e86282 - - - -

Text-mined citations for rs200483245...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Nov 28, 2021