NM_000642.3(AGL):c.1565del (p.Gly522fs) AND Glycogen storage disease type III

Clinical significance:Pathogenic (Last evaluated: Oct 29, 2018)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000820548.1

Allele description [Variation Report for NM_000642.3(AGL):c.1565del (p.Gly522fs)]

NM_000642.3(AGL):c.1565del (p.Gly522fs)

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.1565del (p.Gly522fs)
HGVS:
  • NC_000001.11:g.99877782del
  • NG_012865.1:g.32699del
  • NM_000028.2:c.1565del
  • NM_000642.3:c.1565delMANE SELECT
  • NM_000643.2:c.1565del
  • NM_000644.2:c.1565del
  • NM_000646.2:c.1517del
  • NP_000019.2:p.Gly522fs
  • NP_000633.2:p.Gly522fs
  • NP_000634.2:p.Gly522fs
  • NP_000635.2:p.Gly522fs
  • NP_000637.2:p.Gly506fs
  • NC_000001.10:g.100343338del
  • NM_000642.2:c.1565delG
Protein change:
G506fs
Links:
dbSNP: rs1570438459
NCBI 1000 Genomes Browser:
rs1570438459
Molecular consequence:
  • NM_000028.2:c.1565del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_000642.3:c.1565del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_000643.2:c.1565del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_000644.2:c.1565del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_000646.2:c.1517del - 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

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000961265Invitaecriteria provided, single submitter
Pathogenic
(Oct 29, 2018)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

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):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV000961265.1

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

Description

This sequence change creates a premature translational stop signal (p.Gly522Glufs*14) in the AGL gene. It is expected to result in an absent or disrupted protein product. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with AGL-related disease. Loss-of-function variants in AGL are known to be pathogenic (PMID: 19299494). For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Nov 27, 2021

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