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NM_000642.3(AGL):c.1199T>C (p.Leu400Pro) AND Glycogen storage disease type III

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
May 25, 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:
RCV001351838.6

Allele description [Variation Report for NM_000642.3(AGL):c.1199T>C (p.Leu400Pro)]

NM_000642.3(AGL):c.1199T>C (p.Leu400Pro)

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.1199T>C (p.Leu400Pro)
Other names:
p.Leu400Pro
HGVS:
  • NC_000001.11:g.99875371T>C
  • NG_012865.1:g.30288T>C
  • NM_000028.3:c.1199T>C
  • NM_000642.3:c.1199T>CMANE SELECT
  • NM_000643.3:c.1199T>C
  • NM_000644.3:c.1199T>C
  • NM_000646.3:c.1151T>C
  • NM_001425325.1:c.1199T>C
  • NM_001425326.1:c.1199T>C
  • NM_001425328.1:c.995T>C
  • NM_001425329.1:c.995T>C
  • NM_001425332.1:c.821T>C
  • NP_000019.2:p.Leu400Pro
  • NP_000019.2:p.Leu400Pro
  • NP_000633.2:p.Leu400Pro
  • NP_000634.2:p.Leu400Pro
  • NP_000634.2:p.Leu400Pro
  • NP_000635.2:p.Leu400Pro
  • NP_000635.2:p.Leu400Pro
  • NP_000637.2:p.Leu384Pro
  • NP_000637.2:p.Leu384Pro
  • NP_001412254.1:p.Leu400Pro
  • NP_001412255.1:p.Leu400Pro
  • NP_001412257.1:p.Leu332Pro
  • NP_001412258.1:p.Leu332Pro
  • NP_001412261.1:p.Leu274Pro
  • NC_000001.10:g.100340927T>C
  • NM_000028.2:c.1199T>C
  • NM_000643.2:c.1199T>C
  • NM_000644.2:c.1199T>C
  • NM_000646.2:c.1151T>C
Protein change:
L274P
Links:
dbSNP: rs1275707003
NCBI 1000 Genomes Browser:
rs1275707003
Molecular consequence:
  • NM_000028.3:c.1199T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_000642.3:c.1199T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_000643.3:c.1199T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_000644.3:c.1199T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_000646.3:c.1151T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001425325.1:c.1199T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001425326.1:c.1199T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001425328.1:c.995T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001425329.1:c.995T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001425332.1:c.821T>C - missense variant - [Sequence Ontology: SO:0001583]

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
SCV001546340Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(May 25, 2022) 		germlineclinical testing

PubMed (3)
[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

Molecular analysis of the AGL gene: identification of 25 novel mutations and evidence of genetic heterogeneity in patients with Glycogen Storage Disease Type III.

Goldstein JL, Austin SL, Boyette K, Kanaly A, Veerapandiyan A, Rehder C, Kishnani PS, Bali DS.

Genet Med. 2010 Jul;12(7):424-30. doi: 10.1097/GIM.0b013e3181d94eaa.

PubMed [citation]
PMID:
20648714

Crystal structure of glycogen debranching enzyme and insights into its catalysis and disease-causing mutations.

Zhai L, Feng L, Xia L, Yin H, Xiang S.

Nat Commun. 2016 Apr 18;7:11229. doi: 10.1038/ncomms11229.

PubMed [citation]
PMID:
27088557
PMCID:
PMC4837477
See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001546340.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

This sequence change replaces leucine, which is neutral and non-polar, with proline, which is neutral and non-polar, at codon 400 of the AGL protein (p.Leu400Pro). This variant is present in population databases (no rsID available, gnomAD 0.01%). This missense change has been observed in individual(s) with clinical features of glycogen storage disease type III (PMID: 20648714). ClinVar contains an entry for this variant (Variation ID: 1047162). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0"). Experimental studies are conflicting or provide insufficient evidence to determine the effect of this variant on AGL function (PMID: 27088557). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

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

Last Updated: Sep 29, 2024