NM_000642.3(AGL):c.276del (p.Gln92fs) AND Glycogen storage disease type III

Clinical significance:Pathogenic (Last evaluated: Apr 24, 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:
RCV000409554.2

Allele description [Variation Report for NM_000642.3(AGL):c.276del (p.Gln92fs)]

NM_000642.3(AGL):c.276del (p.Gln92fs)

Gene:
AGL:amylo-alpha-1, 6-glucosidase, 4-alpha-glucanotransferase [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
1p21.2
Genomic location:
Preferred name:
NM_000642.3(AGL):c.276del (p.Gln92fs)
HGVS:
  • NC_000001.11:g.99861696del
  • NG_012865.1:g.16613del
  • NM_000028.2:c.276del
  • NM_000642.3:c.276delMANE SELECT
  • NM_000643.2:c.276del
  • NM_000644.2:c.276del
  • NM_000646.2:c.228del
  • NP_000019.2:p.Gln92fs
  • NP_000633.2:p.Gln92fs
  • NP_000634.2:p.Gln92fs
  • NP_000635.2:p.Gln92fs
  • NP_000637.2:p.Gln76fs
  • NC_000001.10:g.100327252del
  • NM_000642.2:c.276delG
Protein change:
Q76fs
Links:
dbSNP: rs1057517243
NCBI 1000 Genomes Browser:
rs1057517243
Molecular consequence:
  • NM_000028.2:c.276del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_000642.3:c.276del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_000643.2:c.276del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_000644.2:c.276del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_000646.2:c.228del - frameshift variant - [Sequence Ontology: SO:0001589]

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
SCV000486971Counsylcriteria provided, single submitter
Pathogenic
(Sep 13, 2016)
unknownclinical testing

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

mdi-5618_320494_Counsyl Autosomal and X-linked Recessive Disease Classification criteria (2015).pdf,

Citation Link,

SCV001338431Women's Health and Genetics/Laboratory Corporation of America, LabCorpcriteria provided, single submitter
Pathogenic
(Apr 24, 2020)
germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Citation Link

Summary from all submissions

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

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

Glycogen storage disease type III in the Irish population.

Crushell E, Treacy EP, Dawe J, Durkie M, Beauchamp NJ.

J Inherit Metab Dis. 2010 Dec;33 Suppl 3:S215-8. doi: 10.1007/s10545-010-9096-4. Epub 2010 May 20.

PubMed [citation]
PMID:
20490926
See all PubMed Citations (3)

Details of each submission

From Counsyl, SCV000486971.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV001338431.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

Variant summary: AGL c.276delG (p.Gln92HisfsX16) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. Truncations downstream of this position have been classified as pathogenic by our laboratory. The variant allele was found at a frequency of 8e-06 in 250684 control chromosomes (gnomAD). c.276delG has been reported in the literature in individuals affected with Glycogen Storage Disease Type III (Lucchiari_2002, Crushell_2010). These data indicate that the variant may be associated with disease. At least one publication reports this variant results in <10% of normal AGL activity (Crushell_2010). One ClinVar submitter (evaluation after 2014) cites the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.

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

Last Updated: Nov 27, 2021

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