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NM_000642.3(AGL):c.2681+1G>A

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Interpretation:
Pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
4 (Most recent: Jan 7, 2021)
Last evaluated:
Sep 21, 2020
Accession:
VCV000281229.7
Variation ID:
281229
Description:
single nucleotide variant
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NM_000642.3(AGL):c.2681+1G>A

Allele ID
265466
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
1p21.2
Genomic location
1: 99884704 (GRCh38) GRCh38 UCSC
1: 100350260 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000001.10:g.100350260G>A
NC_000001.11:g.99884704G>A
NG_012865.1:g.39621G>A
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000001.11:99884703:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00020 (A)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00001
1000 Genomes Project 0.00020
The Genome Aggregation Database (gnomAD) 0.00003
Links
ClinGen: CA966854
dbSNP: rs201201443
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 Sep 21, 2020 RCV000377764.9
Pathogenic 1 criteria provided, single submitter Jul 11, 2016 RCV000724650.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
AGL - - GRCh38
GRCh37
1284 1299

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(Jul 11, 2016)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000331829.4
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Pathogenic
(Apr 24, 2020)
criteria provided, single submitter
Method: clinical testing
Glycogen storage disease type III
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV001338430.1
Submitted: (May 13, 2020)
Evidence details
Publications
PubMed (2)
Comment:
Variant summary: AGL c.2681+1G>A is located in a canonical splice-site and is predicted to affect mRNA splicing resulting in a significantly altered protein due to … (more)
Pathogenic
(Sep 21, 2020)
criteria provided, single submitter
Method: clinical testing
Glycogen storage disease type III
Allele origin: germline
Invitae
Accession: SCV000626705.3
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (4)
Comment:
This sequence change affects a donor splice site in intron 20 of the AGL gene. It is expected to disrupt RNA splicing and likely results … (more)
Pathogenic
(Jan 02, 2014)
no assertion criteria provided
Method: clinical testing
Glycogen storage disease type III
Allele origin: unknown
Counsyl
Accession: SCV001132327.1
Submitted: (Aug 05, 2019)
Evidence details
Publications
PubMed (2)

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
Distinct mutations in the glycogen debranching enzyme found in glycogen storage disease type III lead to impairment in diverse cellular functions. Cheng A Human molecular genetics 2009 PMID: 19299494
Clinical, biochemical and genetic features of glycogen debranching enzyme deficiency. Lucchiari S Acta myologica : myopathies and cardiomyopathies : official journal of the Mediterranean Society of Myology 2007 PMID: 17915576
Hepatic and neuromuscular forms of glycogenosis type III: nine mutations in AGL. Lucchiari S Human mutation 2006 PMID: 16705713
Splicing in action: assessing disease causing sequence changes. Baralle D Journal of medical genetics 2005 PMID: 16199547
Novel donor splice site mutations of AGL gene in glycogen storage disease type IIIa. Hadjigeorgiou GM Journal of inherited metabolic disease 1999 PMID: 10472540
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=AGL - - - -

Text-mined citations for rs201201443...

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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 27, 2021