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NM_000642.3(AGL):c.2929C>T (p.Arg977Ter)

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Interpretation:
Pathogenic/Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
4 (Most recent: Jan 10, 2022)
Last evaluated:
Jul 15, 2021
Accession:
VCV000370992.5
Variation ID:
370992
Description:
single nucleotide variant
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NM_000642.3(AGL):c.2929C>T (p.Arg977Ter)

Allele ID
357213
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
1p21.2
Genomic location
1: 99891336 (GRCh38) GRCh38 UCSC
1: 100356892 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000001.10:g.100356892C>T
NC_000001.11:g.99891336C>T
NG_012865.1:g.46253C>T
... more HGVS
Protein change
R977*, R961*
Other names
-
Canonical SPDI
NC_000001.11:99891335:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00020 (T)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00000
The Genome Aggregation Database (gnomAD) 0.00003
The Genome Aggregation Database (gnomAD) 0.00001
Trans-Omics for Precision Medicine (TOPMed) 0.00001
1000 Genomes Project 0.00020
Links
ClinGen: CA16040839
dbSNP: rs531425980
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic/Likely pathogenic 4 criteria provided, multiple submitters, no conflicts Jul 15, 2021 RCV000412306.5
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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
1285 1300

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter More information
Likely pathogenic
(Jun 01, 2016)
criteria provided, single submitter
Method: clinical testing
Glycogen storage disease type III
Affected status: unknown
Allele origin: unknown
Counsyl
Accession: SCV000486438.1
Submitted: (Nov 23, 2016)
Publications:
PubMed (3)
PubMed: 269845621799428216705713
Pathogenic
(Sep 22, 2017)
criteria provided, single submitter
Method: clinical testing
Glycogen storage disease type III
Affected status: unknown
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV000918399.1
Submitted: (Apr 24, 2019)
Publications:
PubMed (4)
PubMed: 17994282242574752698456216705713
Comment:
Variant summary: The AGL c.2929C>T (p.Arg977X) variant results in a premature termination codon, predicted to cause a truncated or absent AGL protein due to nonsense … (more)
Pathogenic
(Aug 24, 2020)
criteria provided, single submitter
Method: clinical testing
Glycogen storage disease type III
Affected status: unknown
Allele origin: germline
Invitae
Accession: SCV001211777.2
Submitted: (Jan 07, 2021)
Publications:
PubMed (2)
PubMed: 1670571319299494
Comment:
This sequence change creates a premature translational stop signal (p.Arg977*) in the AGL gene. It is expected to result in an absent or disrupted protein … (more)
Pathogenic
(Jul 15, 2021)
criteria provided, single submitter
Method: clinical testing
Glycogen storage disease type III
Affected status: no
Allele origin: germline
Nilou-Genome Lab
Accession: SCV002055492.1
Submitted: (Jan 10, 2022)

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
Spectrum of AGL mutations in Chinese patients with glycogen storage disease type III: identification of 31 novel mutations. Lu C Journal of human genetics 2016 PMID: 26984562
A mutation analysis of the AGL gene in Korean patients with glycogen storage disease type III. Ko JS Journal of human genetics 2014 PMID: 24257475
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
Elevated serum biotinidase activity in hepatic glycogen storage disorders--a convenient biomarker. Paesold-Burda P Journal of inherited metabolic disease 2007 PMID: 17994282
Hepatic and neuromuscular forms of glycogenosis type III: nine mutations in AGL. Lucchiari S Human mutation 2006 PMID: 16705713

Text-mined citations for rs531425980...

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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 Jan 12, 2022