NM_000642.3(AGL):c.104T>G (p.Leu35Ter) AND Glycogen storage disease type III

Clinical significance:Pathogenic/Likely pathogenic (Last evaluated: Jul 15, 2021)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
4 submissions [Details]
Record status:
current
Accession:
RCV000410214.4

Allele description [Variation Report for NM_000642.3(AGL):c.104T>G (p.Leu35Ter)]

NM_000642.3(AGL):c.104T>G (p.Leu35Ter)

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.104T>G (p.Leu35Ter)
HGVS:
  • NC_000001.11:g.99861524T>G
  • NG_012865.1:g.16441T>G
  • NM_000028.2:c.104T>G
  • NM_000642.3:c.104T>GMANE SELECT
  • NM_000643.2:c.104T>G
  • NM_000644.2:c.104T>G
  • NM_000646.2:c.56T>G
  • NP_000019.2:p.Leu35Ter
  • NP_000633.2:p.Leu35Ter
  • NP_000634.2:p.Leu35Ter
  • NP_000635.2:p.Leu35Ter
  • NP_000637.2:p.Leu19Ter
  • NC_000001.10:g.100327080T>G
  • NM_000642.2:c.104T>G
  • p.Leu35Ter
Protein change:
L19*
Links:
dbSNP: rs1057516567
NCBI 1000 Genomes Browser:
rs1057516567
Molecular consequence:
  • NM_000028.2:c.104T>G - nonsense - [Sequence Ontology: SO:0001587]
  • NM_000642.3:c.104T>G - nonsense - [Sequence Ontology: SO:0001587]
  • NM_000643.2:c.104T>G - nonsense - [Sequence Ontology: SO:0001587]
  • NM_000644.2:c.104T>G - nonsense - [Sequence Ontology: SO:0001587]
  • NM_000646.2:c.56T>G - nonsense - [Sequence Ontology: SO:0001587]
Observations:
1

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
SCV000485881Counsylcriteria provided, single submitter
Likely pathogenic
(Feb 25, 2016)
unknownclinical testing

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

Citation Link,

SCV001482482Centre for Human Geneticscriteria provided, single submitter
Pathogenic
(Feb 25, 2019)
inheritedclinical testing

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

SCV001584151Invitaecriteria provided, single submitter
Pathogenic
(Feb 27, 2020)
germlineclinical testing

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

SCV002055462Nilou-Genome Labcriteria provided, single submitter
Pathogenic
(Jul 15, 2021)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedinheritedyes11not providednot providednot providedclinical testing
not providedgermlinenonot providednot providednot providednot providednot providedclinical testing
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Molecular diagnosis of glycogen storage disease and disorders with overlapping clinical symptoms by massive parallel sequencing.

Vega AI, Medrano C, Navarrete R, Desviat LR, Merinero B, Rodríguez-Pombo P, Vitoria I, Ugarte M, Pérez-Cerdá C, Pérez B.

Genet Med. 2016 Oct;18(10):1037-43. doi: 10.1038/gim.2015.217. Epub 2016 Feb 25.

PubMed [citation]
PMID:
26913919

Distinct mutations in the glycogen debranching enzyme found in glycogen storage disease type III lead to impairment in diverse cellular functions.

Cheng A, Zhang M, Okubo M, Omichi K, Saltiel AR.

Hum Mol Genet. 2009 Jun 1;18(11):2045-52. doi: 10.1093/hmg/ddp128. Epub 2009 Mar 19.

PubMed [citation]
PMID:
19299494
PMCID:
PMC2678930
See all PubMed Citations (4)

Details of each submission

From Counsyl, SCV000485881.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From Centre for Human Genetics, SCV001482482.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)

Description

disease causing

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1inheritedyesnot providednot providednot provided1not provided1not provided

From Invitae, SCV001584151.1

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

Description

This sequence change creates a premature translational stop signal (p.Leu35*) in the AGL gene. It is expected to result 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: 26913919). ClinVar contains an entry for this variant (Variation ID: 370535). 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

From Nilou-Genome Lab, SCV002055462.1

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

Last Updated: Jan 12, 2022

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