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NM_000642.3(AGL):c.1413_1416del (p.Phe471fs) AND Glycogen storage disease type III

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Apr 22, 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:
RCV003633421.1

Allele description [Variation Report for NM_000642.3(AGL):c.1413_1416del (p.Phe471fs)]

NM_000642.3(AGL):c.1413_1416del (p.Phe471fs)

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.1413_1416del (p.Phe471fs)
HGVS:
  • NC_000001.11:g.99876587_99876590del
  • NG_012865.1:g.31504_31507del
  • NM_000028.3:c.1413_1416delTGCT
  • NM_000642.3:c.1413_1416delMANE SELECT
  • NM_000643.3:c.1413_1416delTGCT
  • NM_000644.3:c.1413_1416delTGCT
  • NM_000646.3:c.1365_1368delTGCT
  • NM_001425325.1:c.1413_1416delTGCT
  • NM_001425326.1:c.1413_1416delTGCT
  • NM_001425327.1:c.1212_1215delTGCT
  • NM_001425328.1:c.1209_1212delTGCT
  • NM_001425329.1:c.1209_1212delTGCT
  • NM_001425332.1:c.1035_1038delTGCT
  • NP_000019.2:p.Phe471Leufs
  • NP_000019.2:p.Phe471fs
  • NP_000633.2:p.Phe471fs
  • NP_000634.2:p.Phe471Leufs
  • NP_000634.2:p.Phe471fs
  • NP_000635.2:p.Phe471Leufs
  • NP_000635.2:p.Phe471fs
  • NP_000637.2:p.Phe455Leufs
  • NP_000637.2:p.Phe455fs
  • NP_001412254.1:p.Phe471Leufs
  • NP_001412255.1:p.Phe471Leufs
  • NP_001412256.1:p.Phe404Leufs
  • NP_001412257.1:p.Phe403Leufs
  • NP_001412258.1:p.Phe403Leufs
  • NP_001412261.1:p.Phe345Leufs
  • NC_000001.10:g.100342142_100342145del
  • NC_000001.10:g.100342143_100342146del
  • NM_000028.2:c.1413_1416del
  • NM_000643.2:c.1413_1416del
  • NM_000644.2:c.1413_1416del
  • NM_000646.2:c.1365_1368del
Protein change:
F455fs
Molecular consequence:
  • NM_000028.3:c.1413_1416delTGCT - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_000642.3:c.1413_1416del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_000643.3:c.1413_1416delTGCT - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_000644.3:c.1413_1416delTGCT - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_000646.3:c.1365_1368delTGCT - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001425325.1:c.1413_1416delTGCT - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001425326.1:c.1413_1416delTGCT - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001425327.1:c.1212_1215delTGCT - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001425328.1:c.1209_1212delTGCT - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001425329.1:c.1209_1212delTGCT - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001425332.1:c.1035_1038delTGCT - 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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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004517521Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Apr 22, 2023) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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 Invitae, SCV004517521.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical 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 affected with AGL-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Phe471Leufs*9) 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).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Feb 28, 2024