NM_000642.3(AGL):c.1180G>T (p.Glu394Ter) AND Glycogen storage disease type III

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Oct 24, 2022
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:: RCV000817115.5

Allele description [Variation Report for NM_000642.3(AGL):c.1180G>T (p.Glu394Ter)]

NM_000642.3(AGL):c.1180G>T (p.Glu394Ter)

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.1180G>T (p.Glu394Ter)

HGVS:

NC_000001.11:g.99875251G>T
NG_012865.1:g.30168G>T
NM_000028.3:c.1180G>T
NM_000642.3:c.1180G>TMANE SELECT
NM_000643.3:c.1180G>T
NM_000644.3:c.1180G>T
NM_000646.3:c.1132G>T
NM_001425325.1:c.1180G>T
NM_001425326.1:c.1180G>T
NM_001425328.1:c.976G>T
NM_001425329.1:c.976G>T
NM_001425332.1:c.802G>T
NP_000019.2:p.Glu394Ter
NP_000019.2:p.Glu394Ter
NP_000633.2:p.Glu394Ter
NP_000634.2:p.Glu394Ter
NP_000634.2:p.Glu394Ter
NP_000635.2:p.Glu394Ter
NP_000635.2:p.Glu394Ter
NP_000637.2:p.Glu378Ter
NP_000637.2:p.Glu378Ter
NP_001412254.1:p.Glu394Ter
NP_001412255.1:p.Glu394Ter
NP_001412257.1:p.Glu326Ter
NP_001412258.1:p.Glu326Ter
NP_001412261.1:p.Glu268Ter
NC_000001.10:g.100340807G>T
NM_000028.2:c.1180G>T
NM_000642.2:c.1180G>T
NM_000643.2:c.1180G>T
NM_000644.2:c.1180G>T
NM_000646.2:c.1132G>T

Protein change:

E268*

Links:

dbSNP: rs1570433686

NCBI 1000 Genomes Browser:

rs1570433686

Molecular consequence:

NM_000028.3:c.1180G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_000642.3:c.1180G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_000643.3:c.1180G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_000644.3:c.1180G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_000646.3:c.1132G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001425325.1:c.1180G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001425326.1:c.1180G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001425328.1:c.976G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001425329.1:c.976G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001425332.1:c.802G>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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000957660	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Oct 24, 2022)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 19299494, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000957660

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Oct 24, 2022)

germline

clinical testing

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

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

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

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. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000957660.4

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

Description

This sequence change creates a premature translational stop signal (p.Glu394*) in the AGL gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in AGL are known to be pathogenic (PMID: 19299494). For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 660008). This variant has not been reported in the literature in individuals affected with AGL-related conditions. This variant is not present in population databases (gnomAD no frequency).

#	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: Sep 29, 2024

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