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NM_000642.3(AGL):c.4419dup (p.Thr1474fs) AND Glycogen storage disease type III

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Oct 5, 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:
RCV001932596.4

Allele description [Variation Report for NM_000642.3(AGL):c.4419dup (p.Thr1474fs)]

NM_000642.3(AGL):c.4419dup (p.Thr1474fs)

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.4419dup (p.Thr1474fs)
HGVS:
  • NC_000001.11:g.99916669dup
  • NG_012865.1:g.71586dup
  • NM_000028.3:c.4419dup
  • NM_000642.3:c.4419dupMANE SELECT
  • NM_000643.3:c.4419dup
  • NM_000644.3:c.4419dup
  • NM_000646.3:c.4371dup
  • NM_001425325.1:c.4419dup
  • NM_001425326.1:c.4398dup
  • NM_001425327.1:c.4218dup
  • NM_001425328.1:c.4215dup
  • NM_001425329.1:c.4080dup
  • NM_001425332.1:c.4041dup
  • NP_000019.2:p.Thr1474Tyrfs
  • NP_000019.2:p.Thr1474fs
  • NP_000633.2:p.Thr1474fs
  • NP_000634.2:p.Thr1474Tyrfs
  • NP_000634.2:p.Thr1474fs
  • NP_000635.2:p.Thr1474Tyrfs
  • NP_000635.2:p.Thr1474fs
  • NP_000637.2:p.Thr1458Tyrfs
  • NP_000637.2:p.Thr1458fs
  • NP_001412254.1:p.Thr1474Tyrfs
  • NP_001412255.1:p.Thr1467Tyrfs
  • NP_001412256.1:p.Thr1407Tyrfs
  • NP_001412257.1:p.Thr1406Tyrfs
  • NP_001412258.1:p.Thr1361Tyrfs
  • NP_001412261.1:p.Thr1348Tyrfs
  • NC_000001.10:g.100382224_100382225insT
  • NC_000001.10:g.100382225dup
  • NM_000028.2:c.4419dup
  • NM_000643.2:c.4419dup
  • NM_000644.2:c.4419dup
  • NM_000646.2:c.4371dup
Protein change:
T1458fs
Links:
dbSNP: rs2100876312
NCBI 1000 Genomes Browser:
rs2100876312
Molecular consequence:
  • NM_000028.3:c.4419dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_000642.3:c.4419dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_000643.3:c.4419dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_000644.3:c.4419dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_000646.3:c.4371dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001425325.1:c.4419dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001425326.1:c.4398dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001425327.1:c.4218dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001425328.1:c.4215dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001425329.1:c.4080dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001425332.1:c.4041dup - 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
SCV002127684Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Oct 5, 2022) 		germlineclinical testing

PubMed (5)
[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

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 Labcorp Genetics (formerly Invitae), Labcorp, SCV002127684.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (5)

Description

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. ClinVar contains an entry for this variant (Variation ID: 1367884). 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.Thr1474Tyrfs*9) in the AGL gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 59 amino acid(s) of the AGL protein.

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

Last Updated: Sep 29, 2024