NM_000151.4(G6PC1):c.231-1G>A AND Glycogen storage disease due to glucose-6-phosphatase deficiency type IA

Clinical significance:Pathogenic/Likely pathogenic (Last evaluated: Aug 24, 2020)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000664578.2

Allele description [Variation Report for NM_000151.4(G6PC1):c.231-1G>A]

NM_000151.4(G6PC1):c.231-1G>A

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.231-1G>A
HGVS:
  • NC_000017.11:g.42903930G>A
  • NG_011808.1:g.8133G>A
  • NM_000151.4:c.231-1G>AMANE SELECT
  • NM_001270397.2:c.231-1G>A
  • LRG_147:g.8133G>A
  • NC_000017.10:g.41055947G>A
  • NM_000151.3:c.231-1G>A
Links:
dbSNP: rs1555559279
NCBI 1000 Genomes Browser:
rs1555559279
Molecular consequence:
  • NM_000151.4:c.231-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001270397.2:c.231-1G>A - splice acceptor variant - [Sequence Ontology: SO:0001574]

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
SCV000788565Counsylcriteria provided, single submitter
Likely pathogenic
(Apr 24, 2017)
unknownclinical testing

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

Citation Link,

SCV001582072Invitaecriteria provided, single submitter
Pathogenic
(Aug 24, 2020)
germlineclinical testing

PubMed (4)
[See all records that cite these PMIDs]

Summary from all submissions

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

Citations

PubMed

Glycogen storage disease type Ia: molecular diagnosis of 51 Japanese patients and characterization of splicing mutations by analysis of ectopically transcribed mRNA from lymphoblastoid cells.

Akanuma J, Nishigaki T, Fujii K, Matsubara Y, Inui K, Takahashi K, Kure S, Suzuki Y, Ohura T, Miyabayashi S, Ogawa E, Iinuma K, Okada S, Narisawa K.

Am J Med Genet. 2000 Mar 13;91(2):107-12.

PubMed [citation]
PMID:
10748407

Splicing in action: assessing disease causing sequence changes.

Baralle D, Baralle M.

J Med Genet. 2005 Oct;42(10):737-48. Review.

PubMed [citation]
PMID:
16199547
PMCID:
PMC1735933
See all PubMed Citations (4)

Details of each submission

From Counsyl, SCV000788565.1

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

From Invitae, SCV001582072.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (4)

Description

This sequence change affects an acceptor splice site in intron 1 of the G6PC gene. It is expected to disrupt RNA splicing and likely results in an absent or disrupted protein product. This variant is not present in population databases (ExAC no frequency). This variant has been observed in individual(s) with glycogen storage disease type Ia (PMID: 10748407, Invitae). In at least one individual the data is consistent with the variant being in trans (on the opposite chromosome) from a pathogenic variant. This variant is also known as IVS1-1G>A. ClinVar contains an entry for this variant (Variation ID: 549978). Experimental studies have shown that this variant disrupts mRNA splicing (PMID: 10748407). Donor and acceptor splice site variants typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in G6PC are known to be pathogenic (PMID: 8182131). 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: Oct 7, 2021

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