NM_000642.3(AGL):c.2039G>A (p.Trp680Ter) AND not provided

Clinical significance:Pathogenic (Last evaluated: Jun 26, 2017)

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:
RCV000578784.2

Allele description [Variation Report for NM_000642.3(AGL):c.2039G>A (p.Trp680Ter)]

NM_000642.3(AGL):c.2039G>A (p.Trp680Ter)

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.2039G>A (p.Trp680Ter)
HGVS:
  • NC_000001.11:g.99881329G>A
  • NG_012865.1:g.36246G>A
  • NM_000028.2:c.2039G>A
  • NM_000642.3:c.2039G>AMANE SELECT
  • NM_000643.2:c.2039G>A
  • NM_000644.2:c.2039G>A
  • NM_000646.2:c.1991G>A
  • NP_000019.2:p.Trp680Ter
  • NP_000633.2:p.Trp680Ter
  • NP_000634.2:p.Trp680Ter
  • NP_000635.2:p.Trp680Ter
  • NP_000637.2:p.Trp664Ter
  • NC_000001.10:g.100346885G>A
  • NM_000642.2:c.2039G>A
Protein change:
W664*; TRP680TER
Links:
OMIM: 610860.0003; dbSNP: rs113994129
NCBI 1000 Genomes Browser:
rs113994129
Molecular consequence:
  • NM_000028.2:c.2039G>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_000642.3:c.2039G>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_000643.2:c.2039G>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_000644.2:c.2039G>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_000646.2:c.1991G>A - nonsense - [Sequence Ontology: SO:0001587]
Observations:
1

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000226440EGL Genetic Diagnostics, Eurofins Clinical Diagnosticscriteria provided, single submitter
Pathogenic
(Jun 13, 2014)
germlineclinical testing

Citation Link,

SCV000680765GeneDxcriteria provided, single submitter
Pathogenic
(Jun 26, 2017)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknown1not providednot providednot providednot providedclinical testing

Details of each submission

From EGL Genetic Diagnostics, Eurofins Clinical Diagnostics, SCV000226440.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided1not providednot providednot provided

From GeneDx, SCV000680765.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The W680X nonsense variant in the AGL gene has been reported previously in association with glycogen storage disease type IIIb in an individual compound heterozygous with a pathogenic variant on the opposite allele (Shen et al., 1996). However, W680X has also been reported in four homozygous individuals with hepatomegaly, mild or no cardiac involvement, mild skeletal myopathy, and elevated CK levels, suggesting more of a type IIIa phenotype (Sentner et al., 2013). This pathogenic variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. Therefore, W680X is interpreted to be pathogenic.

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

Last Updated: Nov 27, 2021

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