NM_000642.3(AGL):c.1533dup (p.Tyr512fs) AND Glycogen storage disease type III

Clinical significance:Pathogenic (Last evaluated: Aug 31, 2017)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000631124.1

Allele description [Variation Report for NM_000642.3(AGL):c.1533dup (p.Tyr512fs)]

NM_000642.3(AGL):c.1533dup (p.Tyr512fs)

Gene:
AGL:amylo-alpha-1, 6-glucosidase, 4-alpha-glucanotransferase [Gene - OMIM - HGNC]
Variant type:
Duplication
Cytogenetic location:
1p21.2
Genomic location:
Preferred name:
NM_000642.3(AGL):c.1533dup (p.Tyr512fs)
HGVS:
  • NC_000001.11:g.99877750dup
  • NG_012865.1:g.32667dup
  • NM_000028.2:c.1533dup
  • NM_000642.3:c.1533dupMANE SELECT
  • NM_000643.2:c.1533dup
  • NM_000644.2:c.1533dup
  • NM_000646.2:c.1485dup
  • NP_000019.2:p.Tyr512fs
  • NP_000633.2:p.Tyr512fs
  • NP_000634.2:p.Tyr512fs
  • NP_000635.2:p.Tyr512fs
  • NP_000637.2:p.Tyr496fs
  • NC_000001.10:g.100343306dup
  • NM_000642.2:c.1533dupA
Protein change:
Y496fs
Links:
dbSNP: rs776733170
NCBI 1000 Genomes Browser:
rs776733170
Molecular consequence:
  • NM_000028.2:c.1533dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_000642.3:c.1533dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_000643.2:c.1533dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_000644.2:c.1533dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_000646.2:c.1485dup - 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
SCV000752119Invitaecriteria provided, single submitter
Pathogenic
(Aug 31, 2017)
germlineclinical testing

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

Summary from all submissions

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

Citations

PubMed

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

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV000752119.1

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

Description

This sequence change creates a premature translational stop signal (p.Tyr512Ilefs*3) in the AGL gene. It is expected to result in an absent or disrupted protein product. This variant is present in population databases (rs776733170, ExAC 0.001%). This variant has been reported in combination with another variant in the AGL gene in an individual affected with glycogen storage disease type III (PMID: 20490926). Loss-of-function variants in AGL are known to be pathogenic (PMID: 19299494). For these reasons, this variant has been 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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