NM_000642.3(AGL):c.854del (p.Arg285fs) AND Glycogen storage disease type III

Clinical significance:Pathogenic/Likely pathogenic (Last evaluated: Jul 15, 2021)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
3 submissions [Details]
Record status:
current
Accession:
RCV000671568.4

Allele description [Variation Report for NM_000642.3(AGL):c.854del (p.Arg285fs)]

NM_000642.3(AGL):c.854del (p.Arg285fs)

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.854del (p.Arg285fs)
HGVS:
  • NC_000001.11:g.99870765del
  • NG_012865.1:g.25682del
  • NM_000028.2:c.854del
  • NM_000642.3:c.854delMANE SELECT
  • NM_000643.2:c.854del
  • NM_000644.2:c.854del
  • NM_000646.2:c.806del
  • NP_000019.2:p.Arg285fs
  • NP_000633.2:p.Arg285fs
  • NP_000634.2:p.Arg285fs
  • NP_000635.2:p.Arg285fs
  • NP_000637.2:p.Arg269fs
  • NC_000001.10:g.100336321del
  • NM_000642.2:c.854del
  • NM_000642.2:c.854delG
Protein change:
R269fs
Links:
dbSNP: rs1553184620
NCBI 1000 Genomes Browser:
rs1553184620
Molecular consequence:
  • NM_000028.2:c.854del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_000642.3:c.854del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_000643.2:c.854del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_000644.2:c.854del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_000646.2:c.806del - 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
SCV000796556Counsylcriteria provided, single submitter
Likely pathogenic
(Dec 24, 2017)
unknownclinical testing

Citation Link,

SCV001379995Invitaecriteria provided, single submitter
Pathogenic
(Aug 24, 2019)
germlineclinical testing

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

SCV002055473Nilou-Genome Labcriteria provided, single submitter
Pathogenic
(Jul 15, 2021)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenonot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedunknownunknownnot 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):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818
See all PubMed Citations (3)

Details of each submission

From Counsyl, SCV000796556.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From Invitae, SCV001379995.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

This sequence change creates a premature translational stop signal (p.Arg285Glnfs*3) 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 conditions. ClinVar contains an entry for this variant (Variation ID: 555703). 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

From Nilou-Genome Lab, SCV002055473.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenonot providednot providednot providednot providednot providednot providednot provided

Last Updated: Jan 12, 2022

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