NM_000151.4(G6PC1):c.479G>A (p.Trp160Ter) AND Glycogen storage disease due to glucose-6-phosphatase deficiency type IA

Clinical significance:Likely pathogenic (Last evaluated: Oct 17, 2019)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001193577.1

Allele description [Variation Report for NM_000151.4(G6PC1):c.479G>A (p.Trp160Ter)]

NM_000151.4(G6PC1):c.479G>A (p.Trp160Ter)

Gene:
G6PC1:glucose-6-phosphatase catalytic subunit 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
17q21.31
Genomic location:
Preferred name:
NM_000151.4(G6PC1):c.479G>A (p.Trp160Ter)
HGVS:
  • NC_000017.11:g.42909335G>A
  • NG_011808.1:g.13538G>A
  • NM_000151.4:c.479G>AMANE SELECT
  • NM_001270397.2:c.402G>A
  • NP_000142.2:p.Trp160Ter
  • NP_001257326.1:p.Leu134=
  • LRG_147:g.13538G>A
  • NC_000017.10:g.41061352G>A
  • NM_000151.3:c.479G>A
Protein change:
W160*
Molecular consequence:
  • NM_000151.4:c.479G>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001270397.2:c.402G>A - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:
Glycogen storage disease due to glucose-6-phosphatase deficiency type IA (GSD1A)
Synonyms:
GSD Ia; Glycogen storage disease type 1A; Von Gierke disease; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0009287; MedGen: C2919796; Orphanet: 364; Orphanet: 79258; OMIM: 232200

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001362496Women's Health and Genetics/Laboratory Corporation of America, LabCorpcriteria provided, single submitter
Likely pathogenic
(Oct 17, 2019)
germlineclinical testing

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

Citation Link

Summary from all submissions

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

Citations

PubMed

Molecular diagnosis of glycogen storage disease type I: a review.

Beyzaei Z, Geramizadeh B.

EXCLI J. 2019;18:30-46. Review.

PubMed [citation]
PMID:
30956637
PMCID:
PMC6449677

Rapid detection of glycogen storage disease type Ia by DNA microarray.

Xu S, Qin S, Gu X, Qiu W, Ye J, Han L, He L.

Clin Chem Lab Med. 2010 Sep;48(9):1229-34. doi: 10.1515/CCLM.2010.244.

PubMed [citation]
PMID:
20509832

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV001362496.1

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

Description

Variant summary: G6PC c.479G>A (p.Trp160X) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. Truncations downstream of this position have been classified as pathogenic by our laboratory (eg. c.508C>T (p.Arg170X), c.1039C>T (p.Gln347X)). The variant was absent in 251484 control chromosomes (gnomAD). c.479G>A has been reported in the literature at least in an individual affected with Glycogen Storage Disease Type Ia (Xu_2010). To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as likely pathogenic.

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

Last Updated: Jun 14, 2021

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