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NM_000151.4(G6PC1):c.247C>A (p.Arg83Ser) AND Glycogen storage disease due to glucose-6-phosphatase deficiency type IA

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Aug 2, 2023
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:
RCV003330449.1

Allele description [Variation Report for NM_000151.4(G6PC1):c.247C>A (p.Arg83Ser)]

NM_000151.4(G6PC1):c.247C>A (p.Arg83Ser)

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.247C>A (p.Arg83Ser)
HGVS:
  • NC_000017.11:g.42903947C>A
  • NG_011808.1:g.8150C>A
  • NM_000151.4:c.247C>AMANE SELECT
  • NM_001270397.2:c.247C>A
  • NP_000142.1:p.Arg83Ser
  • NP_000142.2:p.Arg83Ser
  • NP_001257326.1:p.Arg83Ser
  • LRG_147t1:c.247C>A
  • LRG_147:g.8150C>A
  • LRG_147p1:p.Arg83Ser
  • NC_000017.10:g.41055964C>A
  • NM_000151.2:c.247C>A
  • NM_000151.3:c.247C>A
Protein change:
R83S
Molecular consequence:
  • NM_000151.4:c.247C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001270397.2:c.247C>A - missense variant - [Sequence Ontology: SO:0001583]

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

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004039099Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)		Likely pathogenic
(Aug 2, 2023) 		germlineclinical testing

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

Citation Link

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Summary from all submissions

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

Citations

PubMed

Structure-function analysis of human glucose-6-phosphatase, the enzyme deficient in glycogen storage disease type 1a.

Lei KJ, Pan CJ, Liu JL, Shelly LL, Chou JY.

J Biol Chem. 1995 May 19;270(20):11882-6.

PubMed [citation]
PMID:
7744838

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV004039099.1

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

Description

Variant summary: G6PC1 (also known as G6PC) c.247C>A (p.Arg83Ser) results in a non-conservative amino acid change located in the Phosphatidic acid phosphatase type 2/haloperoxidase domain (IPR000326) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 282828 control chromosomes (gnomAD). To our knowledge, no occurrence of c.247C>A in individuals affected with Glycogen Storage Disease Type Ia has been reported. At least one publication reports experimental evidence evaluating an impact on protein function. The most pronounced variant effect results in <10% of normal activity (Lei_1995). In addition, other missense variants in the same residue (R83C, R83H) have been reported in the Human Gene Mutation Database in association with Glycogen Storage Disease Type Ia and classified as pathogenic in our lab. The following publication have been ascertained in the context of this evaluation (PMID: 7744838). No submitters have cited 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: Oct 7, 2023