NM_000642.3(AGL):c.4525C>T (p.Gln1509Ter) AND Glycogen storage disease type III

Clinical significance:Pathogenic (Last evaluated: Sep 15, 2020)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000813231.3

Allele description [Variation Report for NM_000642.3(AGL):c.4525C>T (p.Gln1509Ter)]

NM_000642.3(AGL):c.4525C>T (p.Gln1509Ter)

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.4525C>T (p.Gln1509Ter)
HGVS:
  • NC_000001.11:g.99921577C>T
  • NG_012865.1:g.76494C>T
  • NM_000028.2:c.4525C>T
  • NM_000642.3:c.4525C>TMANE SELECT
  • NM_000643.2:c.4525C>T
  • NM_000644.2:c.4525C>T
  • NM_000646.2:c.4477C>T
  • NP_000019.2:p.Gln1509Ter
  • NP_000633.2:p.Gln1509Ter
  • NP_000634.2:p.Gln1509Ter
  • NP_000635.2:p.Gln1509Ter
  • NP_000637.2:p.Gln1493Ter
  • NC_000001.10:g.100387133C>T
Protein change:
Q1493*
Links:
dbSNP: rs1480850606
NCBI 1000 Genomes Browser:
rs1480850606
Molecular consequence:
  • NM_000028.2:c.4525C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_000642.3:c.4525C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_000643.2:c.4525C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_000644.2:c.4525C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_000646.2:c.4477C>T - nonsense - [Sequence Ontology: SO:0001587]

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
SCV000953580Invitaecriteria provided, single submitter
Pathogenic
(Sep 15, 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

Citations

Details of each submission

From Invitae, SCV000953580.3

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

Description

This sequence change results in a premature translational stop signal in the AGL gene (p.Gln1509*). While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 24 amino acids of the AGL protein. This variant is not present in population databases (ExAC no frequency). This variant has been observed in two siblings in a family suspected with glycogen storage disease type III (Invitae). Experimental studies and prediction algorithms are not available for this variant, and the functional significance of the affected amino acid(s) is currently unknown. This variant disrupts the C-terminus of the AGL protein. Other variant(s) that disrupt this region (p.Tyr1510*) have been determined to be pathogenic (PMID: 8990006, 23430490, 20071996, 20490926, Invitae). This suggests that variants that disrupt this region of the protein are likely to be causative of disease. 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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