NM_000151.4(G6PC1):c.247C>T (p.Arg83Cys)
criteria provided, multiple submitters, no conflicts. Learn more about how ClinVar calculates review status.
Pathogenic (27)
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
-
NM_000151.4(G6PC1):c.247C>T (p.Arg83Cys)
Variation ID: 11998 Accession: VCV000011998.93
- Type and length
-
single nucleotide variant, 1 bp
- Location
-
Cytogenetic: 17q21.31 17: 42903947 (GRCh38) [ NCBI UCSC ] 17: 41055964 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
-
First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Oct 5, 2015 Jun 20, 2026 Jan 24, 2026 - HGVS
-
... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_000151.4:c.247C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000142.2:p.Arg83Cys missense NM_001270397.2:c.247C>T NP_001257326.1:p.Arg83Cys missense NC_000017.11:g.42903947C>T NC_000017.10:g.41055964C>T NG_011808.1:g.8150C>T LRG_147:g.8150C>T LRG_147t1:c.247C>T LRG_147p1:p.Arg83Cys NP_000142.1:p.Arg83Cys P35575:p.Arg83Cys - Protein change
- R83C
- Other names
-
G6PC, ARG83CYS
- Canonical SPDI
- NC_000017.11:42903946:C:T
-
Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
- -
-
Allele frequency
Help
The frequency of the allele represented by this VCV record.
-
The Genome Aggregation Database (gnomAD) 0.00034
Trans-Omics for Precision Medicine (TOPMed) 0.00047
The Genome Aggregation Database (gnomAD), exomes 0.00057
Exome Aggregation Consortium (ExAC) 0.00053
The Genome Aggregation Database (gnomAD) 0.00035
The Genome Aggregation Database (gnomAD), exomes 0.00039
- Links
Genes
| Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
Help
Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
|---|---|---|---|---|---|---|
| HI score
Help
The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
Help
The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
Help
The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
Help
The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
|||
| G6PC1 | - | - |
GRCh38 GRCh37 |
630 | 637 | |
Conditions - Germline
| Condition
Help
The condition for this variant-condition (RCV) record in ClinVar. |
Classification
Help
The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
Help
The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
Help
The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
Help
The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
|---|---|---|---|---|
| Pathogenic (22) |
criteria provided, multiple submitters, no conflicts
|
Jan 24, 2026 | RCV000012778.56 | |
| Pathogenic (1) |
criteria provided, single submitter
|
Jun 6, 2016 | RCV000360229.7 | |
| Pathogenic (4) |
criteria provided, multiple submitters, no conflicts
|
Nov 28, 2025 | RCV000424594.48 | |
| Pathogenic (1) |
criteria provided, single submitter
|
Jan 1, 2017 | RCV000626623.3 | |
| Pathogenic (2) |
criteria provided, multiple submitters, no conflicts
|
Mar 17, 2024 | RCV003987317.5 | |
| Pathogenic (1) |
criteria provided, single submitter
|
Mar 13, 2023 | RCV005357111.1 |
Submissions - Germline
| Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
Help
The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
Help
The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
Expand all rows
Collapse all rows
Help
This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
|
|---|---|---|---|---|---|
|
Pathogenic
(Mar 05, 2018)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
Glycogen storage disease due to glucose-6-phosphatase deficiency type IA |
Genomic Research Center, Shahid Beheshti University of Medical Sciences
Accession: SCV000784537.3
First in ClinVar: May 26, 2018 Last updated: Apr 13, 2025 |
Observation: 1
Collection method: clinical testing
Allele origin: inherited
Affected status: yes
Observation 1
Collection method: clinical testing
Allele origin: inherited
Affected status: yes
Number of individuals with the variant: 1
Age: 0-9 years
Sex: female
Geographic origin: Iran
|
|
|
Pathogenic
(Nov 28, 2025)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
not provided |
Mayo Clinic Laboratories, Mayo Clinic
Accession: SCV000801484.5
First in ClinVar: Aug 04, 2018 Last updated: Jan 11, 2026 |
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
Number of individuals with the variant: 9
|
|
|
Pathogenic
(Jan 24, 2026)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
Glycogen storage disease due to glucose-6-phosphatase deficiency type IA |
Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV000658103.10
First in ClinVar: Dec 26, 2017 Last updated: Mar 07, 2026 |
Comment:
show
This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 83 of the G6PC protein (p.Arg83Cys). This variant is present in population databases (rs1801175, gnomAD 0.7%), including at least one homozygous and/or hemizygous individual. This missense change has been observed in individual(s) with glycogen storage disease (PMID: 7623438, 10834516, 15316959, 18008183, 23312056, 24385852). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It has also been observed to segregate with disease in related individuals. This variant is also known as c.326C>T. ClinVar contains an entry for this variant (Variation ID: 11998). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is expected to disrupt G6PC protein function with a positive predictive value of 95%. Experimental studies have shown that this missense change affects G6PC function (PMID: 7744838). For these reasons, this variant has been classified as Pathogenic. (less)
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
|
|
|
Pathogenic
(Oct 31, 2018)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
Glycogen storage disease due to glucose-6-phosphatase deficiency type IA |
Fulgent Genetics, Fulgent Genetics
Accession: SCV000894121.1
First in ClinVar: Mar 31, 2019 Last updated: Mar 31, 2019 |
Observation: 1
Collection method: clinical testing
Allele origin: unknown
Affected status: unknown
Observation 1
Collection method: clinical testing
Allele origin: unknown
Affected status: unknown
|
|
|
Pathogenic
(Apr 27, 2017)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
Glycogen storage disease due to glucose-6-phosphatase deficiency type IA |
Illumina Laboratory Services, Illumina
Accession: SCV000402976.3
First in ClinVar: Dec 06, 2016 Last updated: May 24, 2019 |
Comment:
show
The G6PC c.247C>T (p.Arg83Cys) variant is widely reported in the literature as a pathogenic variant for glycogen storage disease type I. The variant has been described in several studies as the most prevalent variant for this disease in the Ashkenazi Jewish population (Ekstein et al. 2004; Bali et al. 2006; Froissart et al. 2011). Across eight studies of individuals of different ethnic origins with glycogen storage disease type I, the p.Arg83Cys variant was reported in 35% (110/312) of alleles including at least 25 individuals in whom the variant was found in a homozygous state and seven in whom the variant was found in a compound heterozygous state (Lei et al. 1993; Lei et al. 1994; Lei et al. 1995; Parvari et al. 1997; Rake et al. 2000; Seydewitz et al. 2000; Sever et al. 2012; Carlin et al. 2013). All individuals showed significantly reduced or undetectable enzyme activity in liver biopsy samples. No control data were available from these studies, though the variant is reported at a frequency of 0.00090 in the European (non-Finnish) population of the Exome Aggregation Consortium. Transient expression studies of the variant by Lei et al. (1993) demonstrated that the p.Arg83Cys abolishes enzyme activity. Based on the collective evidence, the p.Arg83Cys variant is classified as pathogenic for glycogen storage disease type I. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. (less)
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
|
|
|
Pathogenic
(Jun 06, 2016)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
Glycogen storage disease
(Autosomal recessive inheritance)
|
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
Accession: SCV000712202.1
First in ClinVar: Apr 09, 2018 Last updated: Apr 09, 2018 |
Comment:
show
The p.Arg83Cys variant in G6PC is the most frequent pathogenic variant implicate d in Glycogen storage disease type I in the Ashkenazi Jewish population (Parvari 1997, Lei 1995, Ekstein 2004). This variant has also been identified 0.09% (60/ 66,646) of European chromosomes by the Exome Aggregation Consortium (ExAC, http: //exac.broadinstitute.org; dbSNP rs1801175). In vitro functional studies also p rovide evidence that the p.Arg83Cys variant may impact protein function (Lei 199 3). In summary, this variant meets our criteria to be classified as pathogenic f or Glycogen storage disease type I in an autosomal recessive manner based upon i ts identification in patients and functional impact. (less)
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: not provided
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: not provided
Number of individuals with the variant: 1
|
|
|
Pathogenic
(May 28, 2019)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
Glycogen storage disease due to glucose-6-phosphatase deficiency type IA |
Mendelics
Accession: SCV001140451.1
First in ClinVar: Jan 13, 2020 Last updated: Jan 13, 2020 |
Observation: 1
Collection method: clinical testing
Allele origin: unknown
Affected status: unknown
Observation 1
Collection method: clinical testing
Allele origin: unknown
Affected status: unknown
|
|
|
Pathogenic
(Oct 18, 2019)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
Glycogen storage disease due to glucose-6-phosphatase deficiency type IA |
Myriad Genetics, Inc.
Accession: SCV001194060.2
First in ClinVar: Apr 06, 2020 Last updated: Jul 06, 2020 |
Comment:
show
NM_000151.3(G6PC):c.247C>T(R83C) is classified as pathogenic in the context of glycogen storage disease type Ia. Sources cited for classification include the following: PMID: 10874313, 12093795, 8734807, 7814621, 15316959, 24082139, 12373566, and 9332655. Classification of NM_000151.3(G6PC):c.247C>T(R83C) is based on the following criteria: This is a well-established pathogenic variant in the literature that has been observed more frequently in patients with clinical diagnoses than in healthy populations. Please note: this variant was assessed in the context of healthy population screening. (less)
Observation: 1
Collection method: clinical testing
Allele origin: unknown
Affected status: unknown
Observation 1
Collection method: clinical testing
Allele origin: unknown
Affected status: unknown
|
|
|
Pathogenic
(Apr 02, 2025)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
Glycogen storage disease due to glucose-6-phosphatase deficiency type IA |
Revvity Omics, Revvity
Accession: SCV002023776.4
First in ClinVar: Nov 29, 2021 Last updated: Sep 06, 2025 |
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
|
|
|
Pathogenic
(Nov 04, 2025)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
Glycogen storage disease type Ia |
Natera, Inc.
Accession: SCV001463398.2
First in ClinVar: Jan 02, 2021 Last updated: Apr 04, 2026 |
Comment:
show
The c.247C>T variant in G6PC1 is a missense variant predicted to cause substitution of arginine to cysteine at amino acid 83. This variant has been observed in one or more individuals affected with the associated recessive disease, as either homozygous or compound heterozygous with a second variant (PMID: 34946936, 12713862). Given the available evidence, this variant is classified as Pathogenic. (less)
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
|
|
|
Pathogenic
(Oct 01, 2025)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
not provided |
CeGaT Center for Human Genetics Tuebingen
Accession: SCV001246604.38
First in ClinVar: May 12, 2020 Last updated: Jun 20, 2026 |
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
Number of individuals with the variant: 8
|
|
|
Pathogenic
(Dec 15, 2014)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
Glycogen storage disease type 1A
(Autosomal recessive inheritance)
|
Knight Diagnostic Laboratories, Oregon Health and Sciences University
Accession: SCV000223927.1
First in ClinVar: Oct 05, 2015 Last updated: Oct 05, 2015 |
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: no
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: no
|
|
|
Pathogenic
(May 13, 2016)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
Glycogen storage disease due to glucose-6-phosphatase deficiency type IA |
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV000695636.1
First in ClinVar: Jan 11, 2018 Last updated: Jan 11, 2018 |
Comment:
show
Variant summary: The G6PC c.247C>T (p.Arg83Cys) variant involves the alteration of a conserved nucleotide resulting in a replacement of and Arginine with a Cystein located in the conserved phosphatase signature motif of G6PC. Mutations of the phosphatase active site residues are known to be clinically relevant; they predispose individuals to Glycogen Storage Disease (Clinvar, HGMD). Consistently, 5/5 in silico tools predict this variant to be deleterious. The variant was found in 64/121294 control chromosomes (1 homozygote) at a frequency of 0.0005276, which does not exceed the estimated maximal expected allele frequency of a pathogenic G6PC variant (0.0017321). It was reported in several GSD patients in either homozygosity or in compound heterozygosity with other pathogenic variant indicating a disease causing impact. A functional study demonstrated the variant to result in complete inactivation of the enzyme, confirming the importance of an intact Arg83 residue in G6Pase catalysis and further supporting pathogenicity. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as Pathogenic. Taken together, this variant is classified as a Pathogenic. (less)
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
|
|
|
Pathogenic
(Jan 01, 2017)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
Hypoglycemia
Short stature |
Centre for Mendelian Genomics, University Medical Centre Ljubljana
Accession: SCV000747324.1
First in ClinVar: May 12, 2018 Last updated: May 12, 2018 |
Observation: 1
Collection method: clinical testing
Allele origin: unknown
Affected status: yes
Observation 1
Collection method: clinical testing
Allele origin: unknown
Affected status: yes
|
|
|
Pathogenic
(-)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
Glycogen storage disease due to glucose-6-phosphatase deficiency type IA |
Pathology and Clinical Laboratory Medicine, King Fahad Medical City
Accession: SCV000996289.1
First in ClinVar: Oct 19, 2019 Last updated: Oct 19, 2019 |
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
Number of individuals with the variant: 8
Ethnicity/Population group: Arab
Geographic origin: Middle East
|
|
|
Pathogenic
(-)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
Glycogen storage disease due to glucose-6-phosphatase deficiency type IA |
Baylor Genetics
Accession: SCV001163780.1
First in ClinVar: Mar 01, 2020 Last updated: Mar 01, 2020 |
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
|
|
|
Pathogenic
(-)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
Glycogen storage disease due to glucose-6-phosphatase deficiency type IA
(Autosomal recessive inheritance)
|
Kids Research, The Children's Hospital at Westmead
Accession: SCV001244747.1
First in ClinVar: May 04, 2020 Last updated: May 04, 2020 |
Observation: 1
Collection method: research
Allele origin: inherited
Affected status: yes
Observation 1
Collection method: research
Allele origin: inherited
Affected status: yes
|
|
|
Pathogenic
(Jan 20, 2022)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
not provided |
GeneDx
Accession: SCV000520992.6
First in ClinVar: Mar 08, 2017 Last updated: Mar 04, 2023 |
Comment:
show
Published functional studies demonstrate loss of glucose-6-phosphatase enzyme activity (Shieh et al., 2002; Chou et al., 2008); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 12713862, 23312056, 8734807, 25333069, 24082139, 8211187, 18449899, 7623438, 15316959, 11739393, 28360385, 28397058, 29365308, 9664612, 30609409, 30202406, 31980526, 32313153, 33224545, 34426522, 34093448, 34258141, 31589614, 33763395, 33101979, 33258288, 31319225) (less)
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
|
|
|
Pathogenic
(Mar 17, 2024)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
not specified |
Genomic Medicine Center of Excellence, King Faisal Specialist Hospital and Research Centre
Accession: SCV004805179.2
First in ClinVar: Mar 30, 2024 Last updated: Apr 06, 2024 |
Observation: 1
Collection method: research
Allele origin: germline
Affected status: unknown
Observation 1
Collection method: research
Allele origin: germline
Affected status: unknown
|
|
|
Pathogenic
(Jun 03, 2022)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
not specified |
Ambry Genetics
Accession: SCV003549547.2
First in ClinVar: Feb 07, 2023 Last updated: May 01, 2024 |
Comment:
show
The c.247C>T (p.R83C) alteration is located in exon 2 (coding exon 2) of the G6PC gene. This alteration results from a C to T substitution at nucleotide position 247, causing the arginine (R) at amino acid position 83 to be replaced by a cysteine (C). Based on data from gnomAD, the T allele has an overall frequency of 0.05% (151/282828) total alleles studied. The highest observed frequency was 0.66% (68/10370) of Ashkenazi Jewish alleles. This alteration has been detected in the homozygous state, and in conjunction with other pathogenic mutations in G6PC1, in multiple individuals with G6PC1-related glycogen storage disease type I (Peeks, 2017; Lei, 1994; Düzenli, 2019; Lei, 1993; Saneifard, 2020; Riley, 2020; Muzetti, 2021; Fang, 2021). It has also been found to segregate in affected individuals in the same family (Carvès, 2003). Another alteration at the same codon, p.R83H (c.248G>A), has been described in individuals with G6PC1-related glycogen storage disease type I (Lei, 1995; Fang, 2021). This amino acid position is highly conserved in available vertebrate species. This alteration is predicted to be deleterious by in silico analysis. Based on the available evidence, this alteration is classified as pathogenic. (less)
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
|
|
|
Pathogenic
(Feb 01, 2024)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
Glycogen storage disease due to glucose-6-phosphatase deficiency type IA |
Laboratory of Medical Genetics, National & Kapodistrian University of Athens
Accession: SCV005051772.1
First in ClinVar: Jun 17, 2024 Last updated: Jun 17, 2024 |
Observation: 1
Collection method: curation
Allele origin: germline
Affected status: no
Observation 1
Collection method: curation
Allele origin: germline
Affected status: no
|
|
|
Pathogenic
(Dec 08, 2021)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
Glycogen storage disease due to glucose-6-phosphatase deficiency type IA |
Breakthrough Genomics, Breakthrough Genomics
Accession: SCV005088759.2
First in ClinVar: Aug 04, 2024 Last updated: Aug 25, 2024 |
Comment:
show
This variant was previously reported in patients with glycogen storage disease in homozygous or compound heterozygous state and reported to segregate with glycogen storage disease type 1a in a family [PMID: 8211187, 23312056, 18008183, 15316959, 15316959, 7623438, 24385852, 10834516]. Functional studies suggested that this variant reduces enzyme activity [PMID: 7744838, 11739393, 18449899]. (less)
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
|
|
|
Pathogenic
(May 15, 2024)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
Glycogen storage disease due to glucose-6-phosphatase deficiency type IA |
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Accession: SCV005875332.1
First in ClinVar: Mar 11, 2025 Last updated: Mar 11, 2025 |
Comment:
show
The G6PC1 c.247C>T; p.Arg83Cys variant (rs1801175, ClinVar Variation ID: 11998), also known as C326T in the literature, is reported in multiple unrelated individuals with glycogen storage disease who are homozygous or compound heterozygous with another G6PC1 variant (Carves 2003, Chan 2018, Hannah 2022, Lei 1993, Trioche 1998, Qu 1996). This variant is observed in the general population with an overall allele frequency of 0.05% (151/282828 alleles, including 1 homozygote) in the Genome Aggregation Database (v2.1.1). Computational analyses predict that this variant is deleterious (REVEL: 0.829). In support of these predictions, functional analyses have shown the variant protein levels are significantly reduced compared to wild type and the variant protein shows abnormal localization (Plona 2021). Based on available information, this variant is considered to be pathogenic. References: Carves C et al. Gouty tendinitis revealing glycogen storage disease Type Ia in two adolescents. Joint Bone Spine. 2003 Mar;70(2):149-53. PMID: 12713862. Chan YM et al. Case 3-2018: A 5-Month-Old Boy with Hypoglycemia. N Engl J Med. 2018 Jan 25;378(4):381-389. PMID: 29365308. Hannah WB et al. Very early-onset inflammatory bowel disease: Novel description in glycogen storage disease type Ia. Mol Genet Metab Rep. 2022 Feb 15;31:100848. PMID: 35242580. Lei KJ et al. Mutations in the glucose-6-phosphatase gene that cause glycogen storage disease type 1a. Science. 1993 Oct 22;262(5133):580-3. PMID: 8211187. Plona KL et al. Classifying molecular phenotypes of G6PC variants for pathogenic properties and to guide therapeutic development. JIMD Rep. 2021 Mar 28;60(1):56-66. PMID: 34258141. Trioche P et al. Prenatal diagnosis of glycogen storage disease type Ia by restriction enzyme digestion. Prenat Diagn. 1998 Jun;18(6):629-31. PMID: 9664612. Qu Y et al. Molecular prenatal diagnosis of glycogen storage disease type Ia. Prenat Diagn. 1996 Apr;16(4):333-6. PMID: 8734807. (less)
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
|
|
|
Pathogenic
(Jun 27, 2018)
C
Contributing to aggregate classification
|
criteria provided, single submitter
|
not provided |
Eurofins Ntd Llc (ga)
Accession: SCV000227025.6
First in ClinVar: Jun 28, 2015 Last updated: Apr 13, 2025 |
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: unknown
Number of individuals with the variant: 13
Zygosity: 1 Homozygote, 12 Single Heterozygotes
Sex: mixed
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Pathogenic
(Mar 13, 2023)
C
Contributing to aggregate classification
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criteria provided, single submitter
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glycogen storage disease I |
Department of Pathology and Laboratory Medicine, Sinai Health System
Accession: SCV005918132.1
First in ClinVar: Apr 28, 2025 Last updated: Apr 28, 2025 |
Observation: 1
Collection method: research
Allele origin: germline
Affected status: unknown
Observation 1
Collection method: research
Allele origin: germline
Affected status: unknown
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Pathogenic
(Jun 28, 2025)
C
Contributing to aggregate classification
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criteria provided, single submitter
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Glycogen storage disease due to glucose-6-phosphatase deficiency type IA |
Immunogenetics and Transplant Biology Service, University Hospital "Città della Salute e della Scienza di Torino"
Accession: SCV006302916.1
First in ClinVar: Aug 03, 2025 Last updated: Aug 03, 2025 |
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
Clinical Features:
hypoglycemia (present) , hypotonia (present) , seizures (present)
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Pathogenic
(Oct 02, 2025)
C
Contributing to aggregate classification
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criteria provided, single submitter
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Glycogen storage disease due to glucose-6-phosphatase deficiency type IA |
3billion
Accession: SCV002573306.3
First in ClinVar: Sep 17, 2022 Last updated: Jun 20, 2026 |
Comment:
show
The variant is observed at an extremely low frequency in the gnomAD v4.1.0 dataset (total allele frequency: 0.040%). Predicted Consequence/Location: Missense variant Functional studies provide moderate evidence of the variant having a damaging effect on the gene or gene product (PMID: 8211187). In silico tool predictions suggest damaging effect of the variant on gene or gene product [REVEL: 0.83 (>=0.6, sensitivity 0.68 and specificity 0.92); 3Cnet: 0.95 (> 0.75, sensitivity 0.96 and precision 0.92)]. The same nucleotide change resulting in the same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000011998 /PMID: 8211187 /3billion dataset). Different missense changes at the same codon (p.Arg83His, p.Arg83Ser) have been reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000038300, VCV002581673 /PMID: 7655466). Therefore, this variant is classified as Pathogenic according to the recommendation of ACMG/AMP guideline. (less)
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
Platform type: exome sequencing
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Pathogenic
(Aug 30, 2004)
N
Not contributing to aggregate classification
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no assertion criteria provided
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GLYCOGEN STORAGE DISEASE Ia |
OMIM
Accession: SCV000033018.3
First in ClinVar: Apr 04, 2013 Last updated: Jan 11, 2018 |
Observation: 1
Collection method: literature only
Allele origin: germline
Affected status: not provided
Observation 1
Collection method: literature only
Allele origin: germline
Affected status: not provided
Comment on evidence:
Lei et al. (1993) concluded that a patient with type Ia glycogen storage disease (GSD1A; 232200) was a compound heterozygote for 2 different G6PC mutations: … (more)
Lei et al. (1993) concluded that a patient with type Ia glycogen storage disease (GSD1A; 232200) was a compound heterozygote for 2 different G6PC mutations: arg83-to-cys (R83C) and arg295-to-cys (R295C; 613742.0003), located in exons 2 and 5, respectively. The exon 5 mutation came from the father and the exon 2 mutation from the mother. Both mutations were thought to involve a CpG doublet. Lei et al. (1994) demonstrated that the R83C mutant has no detectable phosphohydrolase activity. In a patient originally reported by Burchell and Waddell (1990) as having a novel form of type I glycogen storage disease due to a defect in the 21-kD stabilizing protein SP, Lei et al. (1995) demonstrated that in fact there was an R83C mutation in exon 2 of the G6PC gene. They found the same mutation in both homozygous and heterozygous form in patients with standard GSD type Ia. Qu et al. (1996) performed prenatal diagnosis by chorionic villus sampling in an Ashkenazi Jewish family in which a previous child was homoallelic and both parents were heterozygous for the R83C mutation. Molecular analysis showed that the fetus was not affected. Parvari et al. (1997) found that the R83C mutation was present in all Ashkenazi Jewish patients studied in Israel, suggesting that DNA-based diagnosis may be used as an initial diagnostic step in this population, thus avoiding liver biopsy. Ekstein et al. (2004) tested 20,719 Ashkenazi Jewish subjects for the R83C mutation and identified 290 carriers, giving a carrier frequency of 0.014. The authors noted that this carrier frequency translates into a predicted disease prevalence of 1 in 20,000, 5 times higher than that for the general Caucasian population, confirming a founder effect and elevated frequency of type Ia glycogen storage disease in the Ashkenazi population. They also tested 4,290 Ashkenazi subjects for the Q347X (613742.0004) mutation and found no carriers. Of 30 Ashkenazi Jewish patients with type Ia glycogen storage disease, all were homozygous for the R83C mutation. Ekstein et al. (2004) concluded that R83C is the only prevalent mutation for this disease in the Ashkenazi population. (less)
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Pathogenic
(Jan 06, 2020)
N
Not contributing to aggregate classification
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no assertion criteria provided
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Glycogen storage disease type 1A |
Reproductive Health Research and Development, BGI Genomics
Accession: SCV001142473.1
First in ClinVar: Jan 13, 2020 Last updated: Jan 13, 2020 |
Comment:
show
NM_000151.3:c.247C>T is also known as c.326C>T in the literature. NM_000151.3:c.247C>T in the G6PC gene has an allele frequency of 0.007 in Ashkenazi Jewish subpopulation in the gnomAD database. This variant has been reported to segregate with glycogen storage disease type 1a in a single family (PMID: 8211187) and has been reported as homozygous or in combination with another G6PC variant in individuals affected with glycogen storage disease type 1A (PMID: 23312056). Ekstein et al reported 30 Glycogen storage disease type Ia patient in Ashkenazi Jewish origin. All of them are homozygous of this variant (PMID: 15316959). Experimental studies have shown that this missense change severely reduces enzyme activity of the protein encoded by G6PC (PMID: 7744838). Taken together, we interprete this variant as Pathogenic/Likely pathogenic. ACMG/AMP criteria applied: PS3; PM3_Strong; PP4; PP1. (less)
Observation: 1
Collection method: curation
Allele origin: germline
Affected status: unknown
Observation 1
Collection method: curation
Allele origin: germline
Affected status: unknown
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Likely pathogenic
(Oct 11, 2020)
N
Not contributing to aggregate classification
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no assertion criteria provided
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Glycogen storage disease due to glucose-6-phosphatase deficiency type IA |
Biochemical Molecular Genetic Laboratory, King Abdulaziz Medical City
Accession: SCV001469244.1
First in ClinVar: Jan 26, 2021 Last updated: Jan 26, 2021 |
Observation: 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
Observation 1
Collection method: clinical testing
Allele origin: germline
Affected status: yes
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not provided
(-)
N
Not contributing to aggregate classification
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no classification provided
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Glycogen storage disease due to glucose-6-phosphatase deficiency type IA |
GeneReviews
Accession: SCV000040456.3
First in ClinVar: Apr 04, 2013 Last updated: Oct 01, 2022 |
Observation: 1
Collection method: literature only
Allele origin: germline
Affected status: yes
Observation 1
Collection method: literature only
Allele origin: germline
Affected status: yes
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Citations for germline classification of this variant
Help| Title | Author | Journal | Year | Link |
|---|---|---|---|---|
| Evaluation of Glycogen Storage Patients: Report of Twelve Novel Variants and New Clinical Findings in a Turkish Population. | Ersoy M | Genes | 2021 | PMID: 34946936 |
| Neurological Characteristics of Pediatric Glycogen Storage Disease. | Muzetti JH | Frontiers in endocrinology | 2021 | PMID: 34093448 |
| Clinical and Genetic Spectra of Inherited Liver Disease in Children in China. | Fang Y | Frontiers in pediatrics | 2021 | PMID: 33763395 |
| Glycogen Storage Disease Type I. | Adam MP | - | 2021 | PMID: 20301489 |
| A Rare Case of Glycogen Storage Disease Type 1a Presenting with Hemophagocytic Lymphohistiocytosis (HLH). | Saneifard H | Case reports in pediatrics | 2020 | PMID: 33224545 |
| The diagnostic utility of genome sequencing in a pediatric cohort with suspected mitochondrial disease. | Riley LG | Genetics in medicine : official journal of the American College of Medical Genetics | 2020 | PMID: 32313153 |
| Hemophagocytic Lymphohystiocytosis Associated With Type Ia Glycogen Storage Disease. | Düzenli Kar Y | Journal of pediatric hematology/oncology | 2019 | PMID: 29750741 |
| Clinical and biochemical heterogeneity between patients with glycogen storage disease type IA: the added value of CUSUM for metabolic control. | Peeks F | Journal of inherited metabolic disease | 2017 | PMID: 28397058 |
| Regression of hepatocellular adenomas with strict dietary therapy in patients with glycogen storage disease type I. | Beegle RD | JIMD reports | 2015 | PMID: 25308557 |
| Determining mutations in G6PC and SLC37A4 genes in a sample of Brazilian patients with glycogen storage disease types Ia and Ib. | Carlin MP | Genetics and molecular biology | 2013 | PMID: 24385852 |
| Personalized genomic disease risk of volunteers. | Gonzalez-Garay ML | Proceedings of the National Academy of Sciences of the United States of America | 2013 | PMID: 24082139 |
| Glycogen storage disease type Ia: linkage of glucose, glycogen, lactic acid, triglyceride, and uric acid metabolism. | Sever S | Journal of clinical lipidology | 2012 | PMID: 23312056 |
| Glucose-6-phosphatase deficiency. | Froissart R | Orphanet journal of rare diseases | 2011 | PMID: 21599942 |
| Mutation spectrum of glycogen storage disease type Ia in Tunisia: implication for molecular diagnosis. | Barkaoui E | Journal of inherited metabolic disease | 2007 | PMID: 18008183 |
| Mutation frequencies for glycogen storage disease Ia in the Ashkenazi Jewish population. | Ekstein J | American journal of medical genetics. Part A | 2004 | PMID: 15316959 |
| Gouty tendinitis revealing glycogen storage disease Type Ia in two adolescents. | Carvès C | Joint bone spine | 2003 | PMID: 12713862 |
| Glycogen storage disease type I: diagnosis and phenotype/genotype correlation. | Matern D | European journal of pediatrics | 2002 | PMID: 12373566 |
| The catalytic center of glucose-6-phosphatase. HIS176 is the nucleophile forming the phosphohistidine-enzyme intermediate during catalysis. | Ghosh A | The Journal of biological chemistry | 2002 | PMID: 12093795 |
| The molecular basis of glycogen storage disease type 1a: structure and function analysis of mutations in glucose-6-phosphatase. | Shieh JJ | The Journal of biological chemistry | 2002 | PMID: 11739393 |
| Glycogen storage disease type Ia: molecular study in Brazilian patients. | de C Reis F | Journal of human genetics | 2001 | PMID: 11310582 |
| Identification of mutations in the glucose-6-phosphatase gene in Czech and Slovak patients with glycogen storage disease type ia, including novel mutations K76N, V166A and 540del5. | Kozák L | Human mutation | 2000 | PMID: 10874313 |
| Glycogen storage disease type Ia: recent experience with mutation analysis, a summary of mutations reported in the literature and a newly developed diagnostic flow chart. | Rake JP | European journal of pediatrics | 2000 | PMID: 10834516 |
| Molecular genetic analysis of 40 patients with glycogen storage disease type Ia: 100% mutation detection rate and 5 novel mutations. | Seydewitz HH | Human mutation | 2000 | PMID: 10612834 |
| Glycogen storage disease type 1a in Israel: biochemical, clinical, and mutational studies. | Parvari R | American journal of medical genetics | 1997 | PMID: 9332655 |
| Molecular prenatal diagnosis of glycogen storage disease type Ia. | Qu Y | Prenatal diagnosis | 1996 | PMID: 8734807 |
| Mutations in the glucose-6-phosphatase gene are associated with glycogen storage disease types 1a and 1aSP but not 1b and 1c. | Lei KJ | The Journal of clinical investigation | 1995 | PMID: 7814621 |
| Structure-function analysis of human glucose-6-phosphatase, the enzyme deficient in glycogen storage disease type 1a. | Lei KJ | The Journal of biological chemistry | 1995 | PMID: 7744838 |
| Glucose-6-phosphatase gene G327A mutation is common in Chinese patients with glycogen storage disease type Ia. | Hwu WL | Human molecular genetics | 1995 | PMID: 7655466 |
| Characterization of the mutations in the glucose-6-phosphatase gene in Israeli patients with glycogen storage disease type 1a: R83C in six Jews and a novel V166G mutation in a Muslim Arab. | Parvari R | Journal of inherited metabolic disease | 1995 | PMID: 7623438 |
| Genetic basis of glycogen storage disease type 1a: prevalent mutations at the glucose-6-phosphatase locus. | Lei KJ | American journal of human genetics | 1995 | PMID: 7573034 |
| Identification of mutations in the gene for glucose-6-phosphatase, the enzyme deficient in glycogen storage disease type 1a. | Lei KJ | The Journal of clinical investigation | 1994 | PMID: 8182131 |
| Mutations in the glucose-6-phosphatase gene that cause glycogen storage disease type 1a. | Lei KJ | Science (New York, N.Y.) | 1993 | PMID: 8211187 |
| Diagnosis of a novel glycogen storage disease: type 1aSP. | Burchell A | Journal of inherited metabolic disease | 1990 | PMID: 2172641 |
| http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=G6PC | - | - | - | - |
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Text-mined citations for rs1801175 ...
HelpRecord last updated Jun 20, 2026
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.
