NM_000642.3(AGL):c.4258_4259insGGAGATTCCTTAAAGAACTAAAAGTAGGCTCNNNNNAAAAAGAAAACTTTAGATCCAG (p.Asp1420fs) AND Glycogen storage disease type III

Clinical significance:Pathogenic (Last evaluated: Sep 25, 2020)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001385243.1

Allele description [Variation Report for NM_000642.3(AGL):c.4258_4259insGGAGATTCCTTAAAGAACTAAAAGTAGGCTCNNNNNAAAAAGAAAACTTTAGATCCAG (p.Asp1420fs)]

NM_000642.3(AGL):c.4258_4259insGGAGATTCCTTAAAGAACTAAAAGTAGGCTCNNNNNAAAAAGAAAACTTTAGATCCAG (p.Asp1420fs)

Gene:
AGL:amylo-alpha-1, 6-glucosidase, 4-alpha-glucanotransferase [Gene - OMIM - HGNC]
Variant type:
Insertion
Cytogenetic location:
1p21.2
Genomic location:
Preferred name:
NM_000642.3(AGL):c.4258_4259insGGAGATTCCTTAAAGAACTAAAAGTAGGCTCNNNNNAAAAAGAAAACTTTAGATCCAG (p.Asp1420fs)
HGVS:
  • NC_000001.11:g.99915485_99915486insGGAGATTCCTTAAAGAACTAAAAGTAGGCTCNNNNNAAAAAGAAAACTTTAGATCCAG
  • NG_012865.1:g.70402_70403insGGAGATTCCTTAAAGAACTAAAAGTAGGCTCNNNNNAAAAAGAAAACTTTAGATCCAG
  • NM_000028.2:c.4258_4259insGGAGATTCCTTAAAGAACTAAAAGTAGGCTCNNNNNAAAAAGAAAACTTTAGATCCAG
  • NM_000642.3:c.4258_4259insGGAGATTCCTTAAAGAACTAAAAGTAGGCTCNNNNNAAAAAGAAAACTTTAGATCCAGMANE SELECT
  • NM_000643.2:c.4258_4259insGGAGATTCCTTAAAGAACTAAAAGTAGGCTCNNNNNAAAAAGAAAACTTTAGATCCAG
  • NM_000644.2:c.4258_4259insGGAGATTCCTTAAAGAACTAAAAGTAGGCTCNNNNNAAAAAGAAAACTTTAGATCCAG
  • NM_000646.2:c.4210_4211insGGAGATTCCTTAAAGAACTAAAAGTAGGCTCNNNNNAAAAAGAAAACTTTAGATCCAG
  • NP_000019.2:p.Asp1420fs
  • NP_000633.2:p.Asp1420fs
  • NP_000634.2:p.Asp1420fs
  • NP_000635.2:p.Asp1420fs
  • NP_000637.2:p.Asp1404fs
  • NC_000001.10:g.100381024_100381025insGAAAACTTTAGATCCAGGGAGATTCCTTAAAGAACTAAAAGTAGGCTCNNNNNAAAAA
  • NC_000001.10:g.100381041_100381042insGGAGATTCCTTAAAGAACTAAAAGTAGGCTCNNNNNAAAAAGAAAACTTTAGATCCAG
Protein change:
D1404fs
Links:
Molecular consequence:
  • NM_000028.2:c.4258_4259insGGAGATTCCTTAAAGAACTAAAAGTAGGCTCNNNNNAAAAAGAAAACTTTAGATCCAG - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_000642.3:c.4258_4259insGGAGATTCCTTAAAGAACTAAAAGTAGGCTCNNNNNAAAAAGAAAACTTTAGATCCAG - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_000643.2:c.4258_4259insGGAGATTCCTTAAAGAACTAAAAGTAGGCTCNNNNNAAAAAGAAAACTTTAGATCCAG - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_000644.2:c.4258_4259insGGAGATTCCTTAAAGAACTAAAAGTAGGCTCNNNNNAAAAAGAAAACTTTAGATCCAG - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_000646.2:c.4210_4211insGGAGATTCCTTAAAGAACTAAAAGTAGGCTCNNNNNAAAAAGAAAACTTTAGATCCAG - 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
SCV001585008Invitaecriteria provided, single submitter
Pathogenic
(Sep 25, 2020)
germlineclinical testing

PubMed (5)
[See all records that cite these PMIDs]

Summary from all submissions

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

Citations

PubMed

The impact of retrotransposons on human genome evolution.

Cordaux R, Batzer MA.

Nat Rev Genet. 2009 Oct;10(10):691-703. doi: 10.1038/nrg2640. Review.

PubMed [citation]
PMID:
19763152
PMCID:
PMC2884099

A mobile threat to genome stability: The impact of non-LTR retrotransposons upon the human genome.

Konkel MK, Batzer MA.

Semin Cancer Biol. 2010 Aug;20(4):211-21. doi: 10.1016/j.semcancer.2010.03.001. Epub 2010 Mar 20. Review.

PubMed [citation]
PMID:
20307669
PMCID:
PMC2925057
See all PubMed Citations (5)

Details of each submission

From Invitae, SCV001585008.1

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

Description

This sequence change inserts a large fragment of DNA, likely a transposable element, in exon 31 of the AGL gene (c.4258_4259ins?), causing a frameshift at codon 1420 (p.Asp1420fs). The exact size and sequence of the insertion cannot be determined by the current assay. However, the insertion 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. Retrotransposon insertions including LINE1 (L1), Alu, and SVA (SINE-VNTR-Alu) have been reported to be disease-causing through disruption of either a coding region or splice site (PMID: 19763152, 20307669, 22406018) and 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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