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NM_000152.5(GAA):c.2512C>T (p.Gln838Ter)

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Interpretation:
Pathogenic​

Review status:
reviewed by expert panel FDA Recognized Database
Submissions:
3 (Most recent: May 29, 2020)
Last evaluated:
May 4, 2020
Accession:
VCV000092479.4
Variation ID:
92479
Description:
single nucleotide variant
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NM_000152.5(GAA):c.2512C>T (p.Gln838Ter)

Allele ID
98388
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
17q25.3
Genomic location
17: 80118223 (GRCh38) GRCh38 UCSC
17: 78092022 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_673t1:c.2512C>T LRG_673p1:p.Gln838*
NC_000017.10:g.78092022C>T
NC_000017.11:g.80118223C>T
... more HGVS
Protein change
Q838*
Other names
-
Canonical SPDI
NC_000017.11:80118222:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00000
Trans-Omics for Precision Medicine (TOPMed) 0.00001
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00008
Exome Aggregation Consortium (ExAC) 0.00001
Links
ClinGen: CA220400
dbSNP: rs369532274
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 2 reviewed by expert panel May 4, 2020 RCV001200861.2
Pathogenic 1 criteria provided, single submitter Sep 14, 2016 RCV000175263.2
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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
1519 1559

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(May 04, 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: SCV001371718.1
Submitted: (May 29, 2020)
Evidence details
Other databases
https://erepo.clinicalgenome.org…
Comment:
This variant, c.2512C>T (p.Gln838Ter), is a nonsense variant that is predicted to result in nonsense mediated decay and lack of gene product, meeting PVS1. The … (more)
Pathogenic
(Sep 14, 2016)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000226720.5
Submitted: (Jun 30, 2017)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
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: SCV001422608.1
Submitted: (Mar 09, 2020)
Evidence details
Publications
PubMed (1)
Other databases
https://erepo.clinicalgenome.org…
Comment:
The p.Gln838Ter variant in GAA has been reported in 2 African American individuals with Glycogen Storage Disease II, segregated with disease in 2 affected siblings … (more)

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
Immune Tolerance Strategies in Siblings with Infantile Pompe Disease-Advantages for a Preemptive Approach to High-Sustained Antibody Titers. Stenger EO Molecular genetics and metabolism reports 2015 PMID: 26167453
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=GAA - - - -
https://erepo.clinicalgenome.org/evrepo/ui/interpretation/044f7823-3980-446c-97fd-236867eecdaf - - - -
https://erepo.clinicalgenome.org/evrepo/ui/interpretation/ae5da183-9381-4134-a48c-cb6c0262d3f0 - - - -

Text-mined citations for rs369532274...

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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 Oct 08, 2021