NM_000642.3(AGL):c.4500del (p.Pro1501fs) AND Glycogen storage disease type III

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 10, 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:: RCV002857883.2

Allele description [Variation Report for NM_000642.3(AGL):c.4500del (p.Pro1501fs)]

NM_000642.3(AGL):c.4500del (p.Pro1501fs)

Gene:

AGL:amylo-alpha-1, 6-glucosidase, 4-alpha-glucanotransferase [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

1p21.2

Genomic location:

Preferred name:

NM_000642.3(AGL):c.4500del (p.Pro1501fs)

HGVS:

NC_000001.11:g.99921552del
NG_012865.1:g.76469del
NM_000028.3:c.4500delT
NM_000642.3:c.4500delMANE SELECT
NM_000643.3:c.4500delT
NM_000644.3:c.4500delT
NM_000646.3:c.4452delT
NM_001425325.1:c.4500delT
NM_001425326.1:c.4479delT
NM_001425327.1:c.4299delT
NM_001425328.1:c.4296delT
NM_001425329.1:c.4161delT
NM_001425332.1:c.4122delT
NP_000019.2:p.Pro1501Glnfs
NP_000019.2:p.Pro1501fs
NP_000633.2:p.Pro1501fs
NP_000634.2:p.Pro1501Glnfs
NP_000634.2:p.Pro1501fs
NP_000635.2:p.Pro1501Glnfs
NP_000635.2:p.Pro1501fs
NP_000637.2:p.Pro1485Glnfs
NP_000637.2:p.Pro1485fs
NP_001412254.1:p.Pro1501Glnfs
NP_001412255.1:p.Pro1494Glnfs
NP_001412256.1:p.Pro1434Glnfs
NP_001412257.1:p.Pro1433Glnfs
NP_001412258.1:p.Pro1388Glnfs
NP_001412261.1:p.Pro1375Glnfs
NC_000001.10:g.100387107del
NC_000001.10:g.100387108del
NM_000028.2:c.4500del
NM_000643.2:c.4500del
NM_000644.2:c.4500del
NM_000646.2:c.4452del

Protein change:

P1485fs

Molecular consequence:

NM_000028.3:c.4500delT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_000642.3:c.4500del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_000643.3:c.4500delT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_000644.3:c.4500delT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_000646.3:c.4452delT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001425325.1:c.4500delT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001425326.1:c.4479delT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001425327.1:c.4299delT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001425328.1:c.4296delT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001425329.1:c.4161delT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001425332.1:c.4122delT - frameshift variant - [Sequence Ontology: SO:0001589]

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
SCV003228535	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Aug 10, 2022)	germline	clinical testing	PubMed (5) [See all records that cite these PMIDs] 8990006, 20071996, 20490926, 23430490, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003228535

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Aug 10, 2022)

germline

clinical testing

PubMed (5)
[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

A nonsense mutation due to a single base insertion in the 3'-coding region of glycogen debranching enzyme gene associated with a severe phenotype in a patient with glycogen storage disease type IIIa.

Shen J, Bao Y, Chen YT.

Hum Mutat. 1997;9(1):37-40.

PubMed [citation]

PMID:: 8990006

The electrodiagnostic characteristics of Glycogen Storage Disease Type III.

Hobson-Webb LD, Austin SL, Bali DS, Kishnani PS.

Genet Med. 2010 Jul;12(7):440-5. doi: 10.1097/GIM.0b013e3181cd735b.

PubMed [citation]

PMID:: 20071996

See all PubMed Citations (5)

Details of each submission

From Invitae, SCV003228535.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (5)

Description

This sequence change creates a premature translational stop signal (p.Pro1501Glnfs*3) in the AGL gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 32 amino acid(s) of the AGL protein. For these reasons, this variant has been classified as Pathogenic. This variant disrupts a region of the AGL protein in which other variant(s) (p.Tyr1510*) have been determined to be pathogenic (PMID: 8990006, 20071996, 20490926, 23430490). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. 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: Feb 20, 2024

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