NM_000642.3(AGL):c.256C>T (p.Gln86Ter) AND Glycogen storage disease IIIa

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 25, 2017
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV000588509.1

Allele description [Variation Report for NM_000642.3(AGL):c.256C>T (p.Gln86Ter)]

NM_000642.3(AGL):c.256C>T (p.Gln86Ter)

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.256C>T (p.Gln86Ter)

HGVS:

NC_000001.11:g.99861676C>T
NG_012865.1:g.16593C>T
NM_000028.3:c.256C>T
NM_000642.3:c.256C>TMANE SELECT
NM_000643.3:c.256C>T
NM_000644.3:c.256C>T
NM_000646.3:c.208C>T
NM_001425325.1:c.256C>T
NM_001425326.1:c.256C>T
NM_001425327.1:c.256C>T
NM_001425328.1:c.256C>T
NM_001425329.1:c.256C>T
NP_000019.2:p.Gln86Ter
NP_000019.2:p.Gln86Ter
NP_000633.2:p.Gln86Ter
NP_000634.2:p.Gln86Ter
NP_000634.2:p.Gln86Ter
NP_000635.2:p.Gln86Ter
NP_000635.2:p.Gln86Ter
NP_000637.2:p.Gln70Ter
NP_000637.2:p.Gln70Ter
NP_001412254.1:p.Gln86Ter
NP_001412255.1:p.Gln86Ter
NP_001412256.1:p.Gln86Ter
NP_001412257.1:p.Gln86Ter
NP_001412258.1:p.Gln86Ter
NC_000001.10:g.100327232C>T
NM_000028.2:c.256C>T
NM_000642.2:c.256C>T
NM_000643.2:c.256C>T
NM_000644.2:c.256C>T
NM_000646.2:c.208C>T

Protein change:

Q70*

Links:

dbSNP: rs193186112

NCBI 1000 Genomes Browser:

rs193186112

Molecular consequence:

NM_000028.3:c.256C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_000642.3:c.256C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_000643.3:c.256C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_000644.3:c.256C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_000646.3:c.208C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001425325.1:c.256C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001425326.1:c.256C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001425327.1:c.256C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001425328.1:c.256C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001425329.1:c.256C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: Glycogen storage disease IIIa (GSD IIIa)
Identifiers:: MedGen: C1968739

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000697531	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Pathogenic (Aug 25, 2017)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 22899091, 20648714 LabCorp Variant Classification Summary - May 2015.docx Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000697531

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Pathogenic
(Aug 25, 2017)

germline

clinical testing

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

LabCorp Variant Classification Summary - May 2015.docx

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Clinical application of massively parallel sequencing in the molecular diagnosis of glycogen storage diseases of genetically heterogeneous origin.

Wang J, Cui H, Lee NC, Hwu WL, Chien YH, Craigen WJ, Wong LJ, Zhang VW.

Genet Med. 2013 Feb;15(2):106-14. doi: 10.1038/gim.2012.104. Epub 2012 Aug 16.

PubMed [citation]

PMID:: 22899091

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

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000697531.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

Variant summary: The AGL c.256C>T (p.Gln86X) variant results in a premature termination codon, predicted to cause a truncated or absent AGL 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 (e.g. c.3216_3217delGA (p.Glu1072fsX36) and c.4529dupA (p.Tyr1510X)). This variant was found in 3/121018 control chromosomes at a frequency of 0.0000248, which does not exceed the estimated maximal expected allele frequency of a pathogenic AGL variant (0.0022822). Multiple publications have cited the variant in affected individuals. In addition, a clinical diagnostic laboratory classified this variant as pathogenic. Taken together, this variant is classified as pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Mar 16, 2024

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