NM_000642.3(AGL):c.3777_3778delinsAC (p.Trp1259_Met1260delinsTer) AND Glycogen storage disease type III

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Sep 12, 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:: RCV001909801.6

Allele description [Variation Report for NM_000642.3(AGL):c.3777_3778delinsAC (p.Trp1259_Met1260delinsTer)]

NM_000642.3(AGL):c.3777_3778delinsAC (p.Trp1259_Met1260delinsTer)

Gene:

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

Variant type:

Indel

Cytogenetic location:

1p21.2

Genomic location:

Preferred name:

NM_000642.3(AGL):c.3777_3778delinsAC (p.Trp1259_Met1260delinsTer)

HGVS:

NC_000001.11:g.99910788_99910789delinsAC
NG_012865.1:g.65705_65706delinsAC
NM_000028.3:c.3777_3778delGAinsAC
NM_000642.3:c.3777_3778delinsACMANE SELECT
NM_000643.3:c.3777_3778delGAinsAC
NM_000644.3:c.3777_3778delGAinsAC
NM_000646.3:c.3729_3730delGAinsAC
NM_001425325.1:c.3777_3778delGAinsAC
NM_001425326.1:c.3756_3757delGAinsAC
NM_001425327.1:c.3576_3577delGAinsAC
NM_001425328.1:c.3573_3574delGAinsAC
NM_001425329.1:c.3438_3439delGAinsAC
NM_001425332.1:c.3399_3400delGAinsAC
NP_000019.2:p.Trp1259Ter
NP_000019.2:p.Trp1259_Met1260delinsTer
NP_000633.2:p.Trp1259_Met1260delinsTer
NP_000634.2:p.Trp1259Ter
NP_000634.2:p.Trp1259_Met1260delinsTer
NP_000635.2:p.Trp1259Ter
NP_000635.2:p.Trp1259_Met1260delinsTer
NP_000637.2:p.Trp1243Ter
NP_000637.2:p.Trp1243_Met1244delinsTer
NP_001412254.1:p.Trp1259Ter
NP_001412255.1:p.Trp1252Ter
NP_001412256.1:p.Trp1192Ter
NP_001412257.1:p.Trp1191Ter
NP_001412258.1:p.Trp1146Ter
NP_001412261.1:p.Trp1133Ter
NC_000001.10:g.100376344_100376345delinsAC
NM_000028.2:c.3777_3778delinsAC
NM_000643.2:c.3777_3778delinsAC
NM_000644.2:c.3777_3778delinsAC
NM_000646.2:c.3729_3730delinsAC

Protein change:

W1133*

Links:

dbSNP: rs2100849251

NCBI 1000 Genomes Browser:

rs2100849251

Molecular consequence:

NM_000028.3:c.3777_3778delGAinsAC - nonsense - [Sequence Ontology: SO:0001587]
NM_000642.3:c.3777_3778delinsAC - nonsense - [Sequence Ontology: SO:0001587]
NM_000643.3:c.3777_3778delGAinsAC - nonsense - [Sequence Ontology: SO:0001587]
NM_000644.3:c.3777_3778delGAinsAC - nonsense - [Sequence Ontology: SO:0001587]
NM_000646.3:c.3729_3730delGAinsAC - nonsense - [Sequence Ontology: SO:0001587]
NM_001425325.1:c.3777_3778delGAinsAC - nonsense - [Sequence Ontology: SO:0001587]
NM_001425326.1:c.3756_3757delGAinsAC - nonsense - [Sequence Ontology: SO:0001587]
NM_001425327.1:c.3576_3577delGAinsAC - nonsense - [Sequence Ontology: SO:0001587]
NM_001425328.1:c.3573_3574delGAinsAC - nonsense - [Sequence Ontology: SO:0001587]
NM_001425329.1:c.3438_3439delGAinsAC - nonsense - [Sequence Ontology: SO:0001587]
NM_001425332.1:c.3399_3400delGAinsAC - 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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Homo sapiens DDB1 and CUL4 associated factor 4 (DCAF4), transcript variant 8, mR...
Homo sapiens DDB1 and CUL4 associated factor 4 (DCAF4), transcript variant 8, mRNA
gi|1674985913|ref|NM_001352449.2|

Nucleotide
CLUP02_03010 [Colletotrichum lupini]
CLUP02_03010 [Colletotrichum lupini]
Gene ID:73337048

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002185653	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Sep 12, 2022)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 29794575, 19299494, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002185653

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Sep 12, 2022)

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 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

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

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002185653.3

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

Description

For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 1408109). This premature translational stop signal has been observed in individual(s) with glycogen storage disease type III (PMID: 29794575). Information on the frequency of this variant in the gnomAD database is not available, as this variant may be reported differently in the database. This sequence change creates a premature translational stop signal (p.Trp1259*) 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).

#	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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