NM_000642.3(AGL):c.2309-1G>A AND Glycogen storage disease IIIa

Clinical significance:Pathogenic (Last evaluated: Aug 13, 2017)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:

Allele description [Variation Report for NM_000642.3(AGL):c.2309-1G>A]


AGL:amylo-alpha-1, 6-glucosidase, 4-alpha-glucanotransferase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Genomic location:
Preferred name:
  • NC_000001.11:g.99884119G>A
  • NG_012865.1:g.39036G>A
  • NM_000028.2:c.2309-1G>A
  • NM_000642.3:c.2309-1G>AMANE SELECT
  • NM_000643.2:c.2309-1G>A
  • NM_000644.2:c.2309-1G>A
  • NM_000646.2:c.2261-1G>A
  • NC_000001.10:g.100349675G>A
  • NM_000642.2:c.2309-1G>A
dbSNP: rs786204481
NCBI 1000 Genomes Browser:
Molecular consequence:
  • NM_000028.2:c.2309-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_000642.3:c.2309-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_000643.2:c.2309-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_000644.2:c.2309-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_000646.2:c.2261-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]


Glycogen storage disease IIIa (GSD IIIa)
MedGen: C1968739

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
SCV000697530Women's Health and Genetics/Laboratory Corporation of America, LabCorpcriteria provided, single submitter
(Aug 13, 2017)
germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

LabCorp Variant Classification Summary - May 2015.docx

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing



Cross-sectional retrospective study of muscle function in patients with glycogen storage disease type III.

Decostre V, LaforĂȘt P, Nadaj-Pakleza A, De Antonio M, Leveugle S, Ollivier G, Canal A, Kachetel K, Petit F, Eymard B, Behin A, Wahbi K, Labrune P, Hogrel JY.

Neuromuscul Disord. 2016 Sep;26(9):584-92. doi: 10.1016/j.nmd.2016.06.460. Epub 2016 Jun 28.

PubMed [citation]

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, Austin SL, Boyette K, Kanaly A, Veerapandiyan A, Rehder C, Kishnani PS, Bali DS.

Genet Med. 2010 Jul;12(7):424-30. doi: 10.1097/GIM.0b013e3181d94eaa.

PubMed [citation]

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000697530.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)


Variant summary: The c.2309-1G>A (aka IVS17-1G>A) in a AGL gene is a splice-site variant that alters a highly conserved nucleotide. 5/5 in silico tools via Alamut predict this variant to disrupt a canonical acceptor sequence, however these predictions have yet to be confirmed by functional assay. The variant is absent from control dataset of ExAC (~120120 chrs tested), but is present at a low frequency in gnomAD dataset (2/245384 chrs tested). The observed frequency does not exceed the maximum expected allele frequency for a pathogenic variant of 0.00228. The variant has been reported in affected individuals with enzymatically confirmed dx of GSDIII via publications and is cited as Likely Pathogenic by a reputable database/clinical laboratory. Taken together, the variant was classified as Pathogenic.

OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 27, 2021

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