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NM_000642.3(AGL):c.4529dup (p.Tyr1510Ter)

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Interpretation:
Pathogenic/Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
6 (Most recent: Dec 28, 2020)
Last evaluated:
Oct 8, 2018
Accession:
VCV000001094.5
Variation ID:
1094
Description:
1bp duplication
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NM_000642.3(AGL):c.4529dup (p.Tyr1510Ter)

Allele ID
16133
Variant type
Duplication
Variant length
1 bp
Cytogenetic location
1p21.2
Genomic location
1: 99921580-99921581 (GRCh38) GRCh38 UCSC
1: 100387136-100387137 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000001.10:g.100387137dup
NC_000001.11:g.99921581dup
NM_000642.3:c.4529dup MANE Select NP_000633.2:p.Tyr1510Ter nonsense
... more HGVS
Protein change
Y1510*, Y1494*
Other names
-
Canonical SPDI
NC_000001.11:99921580:A:AA
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00006
Exome Aggregation Consortium (ExAC) 0.00002
The Genome Aggregation Database (gnomAD), exomes 0.00002
Links
ClinGen: CA114751
OMIM: 610860.0001
dbSNP: rs387906244
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 3 criteria provided, multiple submitters, no conflicts Oct 8, 2018 RCV000169573.4
Pathogenic 2 criteria provided, single submitter Jan 6, 2017 RCV000001152.4
Pathogenic 1 criteria provided, single submitter Mar 1, 2016 RCV001265666.1
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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
1281 1296

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely pathogenic
(Jan 23, 2015)
criteria provided, single submitter
Method: literature only
Glycogen storage disease type III
(Autosomal recessive inheritance)
Allele origin: unknown
Counsyl
Accession: SCV000221073.1
Submitted: (Mar 11, 2015)
Evidence details
Publications
PubMed (5)
Pathogenic
(Jan 06, 2017)
criteria provided, single submitter
Method: clinical testing
Glycogen storage disease IIIa
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV000697534.1
Submitted: (Jan 25, 2018)
Evidence details
Publications
PubMed (3)
Comment:
Variant summary: The AGL c.4529dupA (p.Tyr1510X) variant results in a premature termination codon, predicted to cause a truncated or absent AGL protein due to nonsense … (more)
Pathogenic
(Oct 08, 2018)
criteria provided, single submitter
Method: clinical testing
Glycogen storage disease type III
Allele origin: germline
Invitae
Accession: SCV000752145.3
Submitted: (Mar 28, 2019)
Evidence details
Publications
PubMed (1)
Comment:
This sequence change results in a premature translational stop signal in the AGL gene (p.Tyr1510*). While this is not anticipated to result in nonsense mediated … (more)
Pathogenic
(Mar 01, 2016)
criteria provided, single submitter
Method: clinical testing
Inborn genetic diseases
Allele origin: germline
Ambry Genetics
Accession: SCV001443833.1
Submitted: (Oct 09, 2020)
Evidence details
Pathogenic
(Jan 01, 1997)
no assertion criteria provided
Method: literature only
GLYCOGEN STORAGE DISEASE, TYPE IIIa
Allele origin: germline
OMIM
Accession: SCV000021302.3
Submitted: (Dec 30, 2010)
Evidence details
Publications
PubMed (1)
Yang, B.-Z., Ding, J.-H., Bao, Y.,  (more...)
Pathogenic
(Sep 16, 2020)
no assertion criteria provided
Method: clinical testing
Glycogen storage disease type III
Allele origin: germline
Natera, Inc.
Accession: SCV001460668.1
Submitted: (Dec 28, 2020)
Evidence details

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
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. Nykamp K Genetics in medicine : official journal of the American College of Medical Genetics 2017 PMID: 28492532
Mutation Analysis in Glycogen Storage Disease Type III Patients in the Netherlands: Novel Genotype-Phenotype Relationships and Five Novel Mutations in the AGL Gene. Sentner CP JIMD reports 2013 PMID: 23430490
Bulbar muscle weakness and fatty lingual infiltration in glycogen storage disorder type IIIa. Horvath JJ Molecular genetics and metabolism 2012 PMID: 23062577
Molecular analysis of the AGL gene: identification of 25 novel mutations and evidence of genetic heterogeneity in patients with Glycogen Storage Disease Type III. Goldstein JL Genetics in medicine : official journal of the American College of Medical Genetics 2010 PMID: 20648714
Glycogen storage disease type III in the Irish population. Crushell E Journal of inherited metabolic disease 2010 PMID: 20490926
A nonsense mutation due to a single base insertion in the 3'-coding region of glycogen debranching enzyme gene associated with a severe phenotype in a patient with glycogen storage disease type IIIa. Shen J Human mutation 1997 PMID: 8990006
Yang, B.-Z., Ding, J.-H., Bao, Y., Eason, J. F. M., Chen, Y.-T. Molecular basis of the enzymatic variability in type III glycogen storage disease (GSD-III). (Abstract) Am. J. Hum. Genet. 51 (suppl.): A28, 1992. - - - -

Text-mined citations for rs387906244...

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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