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NM_000642.3(AGL):c.664+3A>G

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Interpretation:
Pathogenic/Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
5 (Most recent: Jan 7, 2021)
Last evaluated:
Sep 28, 2019
Accession:
VCV000188994.4
Variation ID:
188994
Description:
single nucleotide variant
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NM_000642.3(AGL):c.664+3A>G

Allele ID
186640
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
1p21.2
Genomic location
1: 99864592 (GRCh38) GRCh38 UCSC
1: 100330148 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000001.10:g.100330148A>G
NC_000001.11:g.99864592A>G
NG_012865.1:g.19509A>G
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000001.11:99864591:A:G
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00001
Exome Aggregation Consortium (ExAC) 0.00002
Trans-Omics for Precision Medicine (TOPMed) 0.00002
The Genome Aggregation Database (gnomAD), exomes 0.00002
Trans-Omics for Precision Medicine (TOPMed) 0.00003
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00008
Links
ClinGen: CA274226
dbSNP: rs370792293
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 Sep 28, 2019 RCV000169374.4
Pathogenic 1 criteria provided, single submitter Apr 21, 2017 RCV000585987.1
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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
Likely pathogenic
(Sep 30, 2014)
criteria provided, single submitter
Method: literature only
Glycogen storage disease type III
(Autosomal recessive inheritance)
Allele origin: unknown
Counsyl
Accession: SCV000220754.1
Submitted: (Mar 11, 2015)
Evidence details
Publications
PubMed (3)
Pathogenic
(Apr 21, 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: SCV000697535.1
Submitted: (Jan 25, 2018)
Evidence details
Publications
PubMed (3)
Comment:
Variant summary: The AGL c.664+3A>G variant is an intronic change that involves a conserved nucleotide. 3/5 splice prediction tools predict an impact on normal splicing, … (more)
Pathogenic
(Sep 28, 2019)
criteria provided, single submitter
Method: clinical testing
Glycogen storage disease type III
Allele origin: germline
Invitae
Accession: SCV001382430.2
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (5)
Comment:
This sequence change falls in intron 5 of the AGL gene. It does not directly change the encoded amino acid sequence of the AGL protein, … (more)
Likely pathogenic
(Oct 31, 2014)
no assertion criteria provided
Method: research
Glycogen storage disease type III
Allele origin: germline
Division of Human Genetics,Children's Hospital of Philadelphia
Study: CSER-PediSeq
Accession: SCV000536700.1
Submitted: (Jan 23, 2017)
Evidence details
Publications
PubMed (2)
Pathogenic
(Sep 16, 2020)
no assertion criteria provided
Method: clinical testing
Glycogen storage disease type III
Allele origin: germline
Natera, Inc.
Accession: SCV001454498.1
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
Molecular diagnosis of glycogen storage disease and disorders with overlapping clinical symptoms by massive parallel sequencing. Vega AI Genetics in medicine : official journal of the American College of Medical Genetics 2016 PMID: 26913919
Delayed diagnosis of glycogen storage disease type III. Minen F Journal of pediatric gastroenterology and nutrition 2012 PMID: 21691223
Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization. Buratti E Nucleic acids research 2007 PMID: 17576681
Hepatic and neuromuscular forms of glycogenosis type III: nine mutations in AGL. Lucchiari S Human mutation 2006 PMID: 16705713
Molecular characterisation of GSD III subjects and identification of six novel mutations in AGL. Lucchiari S Human mutation 2002 PMID: 12442284
Statistical features of human exons and their flanking regions. Zhang MQ Human molecular genetics 1998 PMID: 9536098

Text-mined citations for rs370792293...

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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