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

Clinical significance:Likely pathogenic (Last evaluated: Aug 4, 2020)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000169136.2

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

NM_000642.3(AGL):c.2309-1G>A

Gene:
AGL:amylo-alpha-1, 6-glucosidase, 4-alpha-glucanotransferase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1p21.2
Genomic location:
Preferred name:
NM_000642.3(AGL):c.2309-1G>A
HGVS:
  • 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
Links:
dbSNP: rs786204481
NCBI 1000 Genomes Browser:
rs786204481
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]

Condition(s)

Name:
Glycogen storage disease type III (GSD3)
Synonyms:
Glycogen storage disease type 3; Forbes disease; Cori disease; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0009291; MedGen: C0017922; Orphanet: 366; OMIM: 232400

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000220351Counsylcriteria provided, single submitter
Likely pathogenic
(May 27, 2014)
unknownliterature only

PubMed (1)
[See all records that cite this PMID]

Counsyl Autosomal and X-linked Recessive Disease Classification criteria (2015),

Citation Link,

SCV001575138Invitaecriteria provided, single submitter
Likely pathogenic
(Aug 4, 2020)
germlineclinical testing

PubMed (5)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedunknownunknownnot providednot providednot providednot providednot providedliterature only

Citations

PubMed

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]
PMID:
20648714

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]
PMID:
27460348
See all PubMed Citations (5)

Details of each submission

From Counsyl, SCV000220351.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From Invitae, SCV001575138.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (5)

Description

This sequence change affects an acceptor splice site in intron 17 of the AGL gene. It is expected to disrupt RNA splicing and likely results in an absent or disrupted protein product. This variant is not present in population databases (ExAC no frequency). This variant has been observed in individual(s) with glycogen storage disease (PMID: 20648714, 27460348). ClinVar contains an entry for this variant (Variation ID: 188804). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site, but this prediction has not been confirmed by published transcriptional studies. Donor and acceptor splice site variants typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in AGL are known to be pathogenic (PMID: 19299494). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.

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

Last Updated: Nov 27, 2021

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