NM_000642.3(AGL):c.664+3A>G AND Glycogen storage disease type III

Clinical significance:Pathogenic/Likely pathogenic (Last evaluated: Sep 28, 2019)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
4 submissions [Details]
Record status:
current
Accession:
RCV000169374.4

Allele description [Variation Report for NM_000642.3(AGL):c.664+3A>G]

NM_000642.3(AGL):c.664+3A>G

Gene:
AGL:amylo-alpha-1, 6-glucosidase, 4-alpha-glucanotransferase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1p21.2
Genomic location:
Preferred name:
NM_000642.3(AGL):c.664+3A>G
HGVS:
  • NC_000001.11:g.99864592A>G
  • NG_012865.1:g.19509A>G
  • NM_000028.2:c.664+3A>G
  • NM_000642.3:c.664+3A>GMANE SELECT
  • NM_000643.2:c.664+3A>G
  • NM_000644.2:c.664+3A>G
  • NM_000646.2:c.616+3A>G
  • NC_000001.10:g.100330148A>G
  • NM_000642.2:c.664+3A>G
Links:
dbSNP: rs370792293
NCBI 1000 Genomes Browser:
rs370792293
Molecular consequence:
  • NM_000642.3:c.664+3A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000643.2:c.664+3A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000644.2:c.664+3A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000646.2:c.616+3A>G - intron variant - [Sequence Ontology: SO:0001627]

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
SCV000220754Counsylcriteria provided, single submitter
Likely pathogenic
(Sep 30, 2014)
unknownliterature only

PubMed (3)
[See all records that cite these PMIDs]

Counsyl Autosomal and X-linked Recessive Disease Classification criteria (2015),

Citation Link,

SCV000536700Division of Human Genetics,Children's Hospital of Philadelphia - CSER-PediSeqno assertion criteria providedLikely pathogenic
(Oct 31, 2014)
germlineresearch

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

SCV001382430Invitaecriteria provided, single submitter
Pathogenic
(Sep 28, 2019)
germlineclinical testing

PubMed (6)
[See all records that cite these PMIDs]

SCV001454498Natera, Inc.no assertion criteria providedPathogenic
(Sep 16, 2020)
germlineclinical testing

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownunknownnot providednot providednot providednot providednot providedliterature only
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing, research

Citations

PubMed

Hepatic and neuromuscular forms of glycogenosis type III: nine mutations in AGL.

Lucchiari S, Pagliarani S, Salani S, Filocamo M, Di Rocco M, Melis D, Rodolico C, Musumeci O, Toscano A, Bresolin N, Comi GP.

Hum Mutat. 2006 Jun;27(6):600-1.

PubMed [citation]
PMID:
16705713

Delayed diagnosis of glycogen storage disease type III.

Minen F, Cont G, De Cunto A, Martelossi S, Ventura A, Maggiore G, Faletra F, Gasparini P, Cassandrini D.

J Pediatr Gastroenterol Nutr. 2012 Jan;54(1):122-4. doi: 10.1097/MPG.0b013e318228d806. No abstract available.

PubMed [citation]
PMID:
21691223
See all PubMed Citations (6)

Details of each submission

From Counsyl, SCV000220754.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (3)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From Division of Human Genetics,Children's Hospital of Philadelphia - CSER-PediSeq, SCV000536700.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedresearch PubMed (2)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Invitae, SCV001382430.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (6)

Description

This sequence change falls in intron 5 of the AGL gene. It does not directly change the encoded amino acid sequence of the AGL protein, but it affects a nucleotide within the consensus splice site of the intron. This variant is present in population databases (rs370792293, ExAC 0.003%). This variant has been observed in several individuals affected with glycogen storage disease type III (PMID: 16705713, 12442284, 21691223). This variant is also known as IVS6 +3 A>G in the literature. ClinVar contains an entry for this variant (Variation ID: 188994). Nucleotide substitutions within the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Experimental studies have shown that this variant disrupts mRNA splicing (PMID: 12442284). For these reasons, this variant has been classified as Pathogenic.

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

From Natera, Inc., SCV001454498.1

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

Last Updated: Nov 27, 2021

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