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NM_000152.5(GAA):c.1551+1G>T

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Interpretation:
Pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
3 (Most recent: Apr 27, 2021)
Last evaluated:
Apr 8, 2021
Accession:
VCV000555986.3
Variation ID:
555986
Description:
single nucleotide variant
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NM_000152.5(GAA):c.1551+1G>T

Allele ID
548423
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
17q25.3
Genomic location
17: 80110841 (GRCh38) GRCh38 UCSC
17: 78084640 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000017.10:g.78084640G>T
NC_000017.11:g.80110841G>T
NM_000152.5:c.1551+1G>T MANE Select splice donor
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000017.11:80110840:G:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00001
Exome Aggregation Consortium (ExAC) 0.00001
Links
dbSNP: rs770780848
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 3 criteria provided, multiple submitters, no conflicts Apr 8, 2021 RCV000671915.3
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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
(Jan 05, 2018)
criteria provided, single submitter
Method: clinical testing
Glycogen storage disease, type II
Allele origin: unknown
Counsyl
Accession: SCV000796949.1
Submitted: (Jul 10, 2018)
Evidence details
Publications
PubMed (2)
Pathogenic
(Apr 08, 2021)
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: SCV001572465.1
Submitted: (Apr 27, 2021)
Evidence details
Publications
PubMed (6)
Comment:
Variant summary: GAA c.1551+1G>T is located in a canonical splice-site and is predicted to affect mRNA splicing resulting in a significantly altered protein due to … (more)
Likely 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: SCV001422696.1
Submitted: (Mar 09, 2020)
Evidence details
Publications
PubMed (2)
Other databases
https://erepo.clinicalgenome.org…
Comment:
The c.1551+1G>T variant in GAA has been reported in five individuals with glycogen storage disease II, segregated with disease in two affected relatives from one … (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
Lysosomal storage disorders: Novel and frequent pathogenic variants in a large cohort of Indian patients of Pompe, Fabry, Gaucher and Hurler disease. Thomas DC Clinical biochemistry 2021 PMID: 33301762
Clinical and Molecular Disease Spectrum and Outcomes in Patients with Infantile-Onset Pompe Disease. Gupta N The Journal of pediatrics 2020 PMID: 31606152
Clinical characteristics and genotypes in the ADVANCE baseline data set, a comprehensive cohort of US children and adolescents with Pompe disease. Kishnani PS Genetics in medicine : official journal of the American College of Medical Genetics 2019 PMID: 31086307
Late-onset Pompe disease in France: molecular features and epidemiology from a nationwide study. Semplicini C Journal of inherited metabolic disease 2018 PMID: 30155607
Fibromyalgia-like symptoms associated with irritable bowel syndrome: A challenging diagnosis of late-onset Pompe disease. Gesquière-Dando A Muscle & nerve 2015 PMID: 25703594
Identification and characterization of aberrant GAA pre-mRNA splicing in pompe disease using a generic approach. Bergsma AJ Human mutation 2015 PMID: 25243733
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
https://erepo.clinicalgenome.org/evrepo/ui/interpretation/24a65654-6238-40a2-8b67-0932a8597c3a - - - -

Text-mined citations for rs770780848...

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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 Jun 14, 2021