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NM_000642.3(AGL):c.753_756del (p.Asp251fs)

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Interpretation:
Pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
7 (Most recent: Nov 19, 2021)
Last evaluated:
Oct 1, 2020
Accession:
VCV000370509.11
Variation ID:
370509
Description:
4bp deletion
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NM_000642.3(AGL):c.753_756del (p.Asp251fs)

Allele ID
357199
Variant type
Deletion
Variant length
4 bp
Cytogenetic location
1p21.2
Genomic location
1: 99870485-99870488 (GRCh38) GRCh38 UCSC
1: 100336041-100336044 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NM_000642.3:c.750_753delAGAC MANE Select
NC_000001.10:g.100336044_100336047del
NC_000001.11:g.99870488_99870491del
... more HGVS
Protein change
D235fs, D251fs
Other names
-
Canonical SPDI
NC_000001.11:99870484:AGACAGA:AGA
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA966256
dbSNP: rs748789700
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 6 criteria provided, multiple submitters, no conflicts Oct 1, 2020 RCV000409582.12
Pathogenic 1 criteria provided, single submitter Mar 21, 2019 RCV001008814.1
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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
Pathogenic
(Feb 26, 2016)
criteria provided, single submitter
Method: clinical testing
Glycogen storage disease type III
Allele origin: unknown
Counsyl
Accession: SCV000485852.1
Submitted: (Nov 23, 2016)
Evidence details
Publications
PubMed (4)
Pathogenic
(Aug 09, 2018)
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: SCV000918404.1
Submitted: (Apr 24, 2019)
Evidence details
Publications
PubMed (4)
Comment:
Variant summary: AGL c.753_756delCAGA (p.Asp251GlufsX23) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein … (more)
Pathogenic
(Mar 21, 2019)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001168615.1
Submitted: (Oct 15, 2019)
Evidence details
Comment:
The c.753_756delCAGA variant (also reported as 750_753delAGA, due to alternate nomenclature) in the AGL gene has been reported previously in the homozygous state in individuals … (more)
Pathogenic
(-)
criteria provided, single submitter
Method: clinical testing
Glycogen storage disease type III
Allele origin: germline
Centogene AG - the Rare Disease Company
Accession: SCV001424356.1
Submitted: (Jul 14, 2020)
Evidence details
Pathogenic
(Oct 01, 2020)
criteria provided, single submitter
Method: clinical testing
Glycogen storage disease type III
Allele origin: germline
Invitae
Accession: SCV000626766.5
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (6)
Comment:
This sequence change creates a premature translational stop signal (p.Asp251Glufs*23) in the AGL gene. It is expected to result in an absent or disrupted protein … (more)
Pathogenic
(Aug 10, 2021)
no assertion criteria provided
Method: clinical testing
Glycogen storage disease type III
(Autosomal recessive inheritance)
Allele origin: inherited
Centre for Human Genetics
Accession: SCV001976629.1
Submitted: (Sep 27, 2021)
Evidence details
Comment:
disease causing
Pathogenic
(Dec 21, 2019)
no assertion criteria provided
Method: clinical testing
Glycogen storage disease type III
Allele origin: germline
PerkinElmer Genomics
Accession: SCV002023008.1
Submitted: (Nov 19, 2021)
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
Inherent lipid metabolic dysfunction in glycogen storage disease IIIa. Li XH Biochemical and biophysical research communications 2014 PMID: 25451272
Glycogen storage disease type III: modified Atkins diet improves myopathy. Mayorandan S Orphanet journal of rare diseases 2014 PMID: 25431232
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
Phenotypical variability in glycogen storage disease type III with a recurrent AGL mutation c.750-753delAGAC. Okubo M Muscle & nerve 2011 PMID: 21321962
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
Hepatic and neuromuscular forms of glycogenosis type III: nine mutations in AGL. Lucchiari S Human mutation 2006 PMID: 16705713
Molecular characterization of Egyptian patients with glycogen storage disease type IIIa. Endo Y Journal of human genetics 2005 PMID: 16189622

Text-mined citations for rs748789700...

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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 28, 2021