NM_000642.3(AGL):c.1183C>T (p.Gln395Ter) AND Glycogen storage disease type III

This record was updated by the submitter. Please see the current version.

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Apr 28, 2023
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:: RCV003634292.1

Allele description

NM_000642.3(AGL):c.1183C>T (p.Gln395Ter)

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.1183C>T (p.Gln395Ter)

HGVS:

NC_000001.11:g.99875254C>T
NG_012865.1:g.30171C>T
NM_000028.3:c.1183C>T
NM_000642.3:c.1183C>TMANE SELECT
NM_000643.3:c.1183C>T
NM_000644.3:c.1183C>T
NM_000646.3:c.1135C>T
NM_001425325.1:c.1183C>T
NM_001425326.1:c.1183C>T
NM_001425328.1:c.979C>T
NM_001425329.1:c.979C>T
NM_001425332.1:c.805C>T
NP_000019.2:p.Gln395Ter
NP_000019.2:p.Gln395Ter
NP_000633.2:p.Gln395Ter
NP_000634.2:p.Gln395Ter
NP_000634.2:p.Gln395Ter
NP_000635.2:p.Gln395Ter
NP_000635.2:p.Gln395Ter
NP_000637.2:p.Gln379Ter
NP_000637.2:p.Gln379Ter
NP_001412254.1:p.Gln395Ter
NP_001412255.1:p.Gln395Ter
NP_001412257.1:p.Gln327Ter
NP_001412258.1:p.Gln327Ter
NP_001412261.1:p.Gln269Ter
NC_000001.10:g.100340810C>T
NM_000028.2:c.1183C>T
NM_000643.2:c.1183C>T
NM_000644.2:c.1183C>T
NM_000646.2:c.1135C>T

Protein change:

Q269*

Molecular consequence:

NM_000028.3:c.1183C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_000642.3:c.1183C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_000643.3:c.1183C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_000644.3:c.1183C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_000646.3:c.1135C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001425325.1:c.1183C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001425326.1:c.1183C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001425328.1:c.979C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001425329.1:c.979C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001425332.1:c.805C>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
SCV004551480	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Apr 28, 2023)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 19299494, 29794575, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004551480

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Apr 28, 2023)

germline

clinical testing

PubMed (3)
[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

Distinct Clinical and Genetic Findings in Iranian Patients With Glycogen Storage Disease Type 3.

Nazari F, Sinaei F, Nilipour Y, Petit F, Oveisgharan S, Nassiri-Toosi M, Razzaghy-Azar M, Mahmoudi M, Nafissi S.

J Clin Neuromuscul Dis. 2018 Jun;19(4):203-210. doi: 10.1097/CND.0000000000000212.

PubMed [citation]

PMID:: 29794575

See all PubMed Citations (3)

Details of each submission

From Invitae, SCV004551480.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This sequence change creates a premature translational stop signal (p.Gln395*) 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. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. This premature translational stop signal has been observed in individual(s) with glycogen storage disease (PMID: 29794575). 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: Feb 28, 2024

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