NM_000642.3(AGL):c.3756dup (p.Arg1253fs) AND Glycogen storage disease type III

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Apr 5, 2021
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:: RCV001388706.5

Allele description [Variation Report for NM_000642.3(AGL):c.3756dup (p.Arg1253fs)]

NM_000642.3(AGL):c.3756dup (p.Arg1253fs)

Gene:

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

Variant type:

Duplication

Cytogenetic location:

1p21.2

Genomic location:

Preferred name:

NM_000642.3(AGL):c.3756dup (p.Arg1253fs)

HGVS:

NC_000001.11:g.99910767dup
NG_012865.1:g.65684dup
NM_000028.3:c.3756dup
NM_000642.3:c.3756dupMANE SELECT
NM_000643.3:c.3756dup
NM_000644.3:c.3756dup
NM_000646.3:c.3708dup
NM_001425325.1:c.3756dup
NM_001425326.1:c.3735dup
NM_001425327.1:c.3555dup
NM_001425328.1:c.3552dup
NM_001425329.1:c.3417dup
NM_001425332.1:c.3378dup
NP_000019.2:p.Arg1253Serfs
NP_000019.2:p.Arg1253fs
NP_000633.2:p.Arg1253fs
NP_000634.2:p.Arg1253Serfs
NP_000634.2:p.Arg1253fs
NP_000635.2:p.Arg1253Serfs
NP_000635.2:p.Arg1253fs
NP_000637.2:p.Arg1237Serfs
NP_000637.2:p.Arg1237fs
NP_001412254.1:p.Arg1253Serfs
NP_001412255.1:p.Arg1246Serfs
NP_001412256.1:p.Arg1186Serfs
NP_001412257.1:p.Arg1185Serfs
NP_001412258.1:p.Arg1140Serfs
NP_001412261.1:p.Arg1127Serfs
NC_000001.10:g.100376322_100376323insT
NC_000001.10:g.100376323dup
NM_000028.2:c.3756dup
NM_000643.2:c.3756dup
NM_000644.2:c.3756dup
NM_000646.2:c.3708dup

Protein change:

R1237fs

Links:

dbSNP: rs2100849117

NCBI 1000 Genomes Browser:

rs2100849117

Molecular consequence:

NM_000028.3:c.3756dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_000642.3:c.3756dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_000643.3:c.3756dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_000644.3:c.3756dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_000646.3:c.3708dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001425325.1:c.3756dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001425326.1:c.3735dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001425327.1:c.3555dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001425328.1:c.3552dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001425329.1:c.3417dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001425332.1:c.3378dup - 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

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001589781	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Apr 5, 2021)	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

SCV001589781

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Apr 5, 2021)

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, SCV001589781.4

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

Description

For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals with AGL-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change creates a premature translational stop signal (p.Arg1253Serfs*10) 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

ClinVar

Relating variation to medicine