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NM_000152.5(GAA):c.2501_2502del (p.Thr834fs)

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Interpretation:
Pathogenic​

Review status:
reviewed by expert panel FDA Recognized Database
Submissions:
8 (Most recent: Jan 7, 2021)
Last evaluated:
May 5, 2020
Accession:
VCV000286229.8
Variation ID:
286229
Description:
2bp microsatellite
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NM_000152.5(GAA):c.2501_2502del (p.Thr834fs)

Allele ID
270466
Variant type
Microsatellite
Variant length
2 bp
Cytogenetic location
17q25.3
Genomic location
17: 80118210-80118211 (GRCh38) GRCh38 UCSC
17: 78092009-78092010 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000017.10:g.78092009CA[1]
NC_000017.11:g.80118210CA[1]
NM_000152.5:c.2501_2502del MANE Select NP_000143.2:p.Thr834fs frameshift
... more HGVS
Protein change
T834fs
Other names
-
Canonical SPDI
NC_000017.11:80118209:CACA:CA
Functional consequence
RNA degradation by nonsense-mediated decay [Variation Ontology VariO:0347]
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA10605404
dbSNP: rs886043343
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 7 reviewed by expert panel May 5, 2020 RCV000285320.9
Pathogenic 1 criteria provided, single submitter Feb 23, 2016 RCV000725814.1
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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
1499 1538

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: SCV001371719.1
Submitted: (May 29, 2020)
Evidence details
Publications
PubMed (4)
Other databases
https://erepo.clinicalgenome.org…
Comment:
This variant, c.2501_2502delCA (p.Thr834Argfs) is predicted to result in a frameshift causing a premature termination codon, nonsense medicated decay, and lack of GAA gene product, … (more)
Likely pathogenic
(-)
criteria provided, single submitter
Method: clinical testing
Glycogen storage disease, type II
(Autosomal recessive inheritance)
Allele origin: inherited
Tehran Medical Genetics Laboratory
Accession: SCV000692564.1
Submitted: (Apr 28, 2018)
Evidence details
Pathogenic
(Feb 23, 2016)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000339572.4
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Pathogenic
(Nov 30, 2018)
criteria provided, single submitter
Method: clinical testing
Glycogen storage disease, type II
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV000917399.1
Submitted: (Apr 24, 2019)
Evidence details
Publications
PubMed (3)
Comment:
Variant summary: GAA c.2501_2502delCA (p.Thr834ArgfsX49) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein … (more)
Pathogenic
(Jun 17, 2020)
criteria provided, single submitter
Method: clinical testing
Glycogen storage disease, type II
Allele origin: germline
Invitae
Accession: SCV001379737.2
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (6)
Comment:
This sequence change creates a premature translational stop signal (p.Thr834Argfs*49) in the GAA gene. It is expected to result in an absent or disrupted protein … (more)
Pathogenic
(Nov 17, 2016)
no assertion criteria provided
Method: clinical testing
Glycogen storage disease, type II
Allele origin: unknown
Counsyl
Accession: SCV001132394.1
Submitted: (Aug 05, 2019)
Evidence details
Publications
PubMed (1)
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: SCV001423058.1
Submitted: (Mar 09, 2020)
Evidence details
Publications
PubMed (1)
Other databases
https://erepo.clinicalgenome.org…
Comment:
The p.Thr834ArgfsTer49 variant in GAA has been reported in 8 individuals with Glycogen Storage Disease II (PMID: 22958975, 23601496, 29122469, 19588081), and has also been … (more)
Pathogenic
(Sep 16, 2020)
no assertion criteria provided
Method: clinical testing
Glycogen storage disease type II
Allele origin: germline
Natera, Inc.
Accession: SCV001463862.1
Submitted: (Dec 28, 2020)
Evidence details

Functional evidence

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Functional consequence Method Result Submitter Supporting information
RNA degradation by nonsense-mediated decay
Tehran Medical Genetics Laboratory
Accession: SCV000692564.1
Submitted: (Apr 28, 2018)
Evidence details

Citations for this variant

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Title Author Journal Year Link
Genetic landscape and novel disease mechanisms from a large LGMD cohort of 4656 patients. Nallamilli BRR Annals of clinical and translational neurology 2018 PMID: 30564623
Sensitivity of whole exome sequencing in detecting infantile- and late-onset Pompe disease. Mori M Molecular genetics and metabolism 2017 PMID: 29122469
B-Cell depletion and immunomodulation before initiation of enzyme replacement therapy blocks the immune response to acid alpha-glucosidase in infantile-onset Pompe disease. Elder ME The Journal of pediatrics 2013 PMID: 23601496
Auditory system involvement in late onset Pompe disease: a study of 20 Italian patients. Musumeci O Molecular genetics and metabolism 2012 PMID: 22958975
Transcriptional response to GAA deficiency (Pompe disease) in infantile-onset patients. Palermo AT Molecular genetics and metabolism 2012 PMID: 22658377
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
Pompe disease in a Brazilian series: clinical and molecular analyses with identification of nine new mutations. Oba-Shinjo SM Journal of neurology 2009 PMID: 19588081
Update of the Pompe disease mutation database with 107 sequence variants and a format for severity rating. Kroos M Human mutation 2008 PMID: 18425781
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=GAA - - - -
https://erepo.clinicalgenome.org/evrepo/ui/interpretation/57e08dd1-a8d8-451f-81c4-f2ea4f52061f - - - -
https://erepo.clinicalgenome.org/evrepo/ui/interpretation/77174bc5-987b-4b3a-94f0-868d75cd5e60 - - - -

Text-mined citations for rs886043343...

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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 Aug 27, 2021