G6PC1
protein-codingglucose-6-phosphatase catalytic subunit 1, the group of Glucose 6-phosphatases, catalytic
Gene summary
Glucose-6-phosphatase (G6Pase) is a multi-subunit integral membrane protein of the endoplasmic reticulum that is composed of a catalytic subunit and transporters for G6P, inorganic phosphate, and glucose. This gene (G6PC) is one of the three glucose-6-phosphatase catalytic-subunit-encoding genes in human: G6PC, G6PC2 and G6PC3. Glucose-6-phosphatase catalyzes the hydrolysis of D-glucose 6-phosphate to D-glucose and orthophosphate and is a key enzyme in glucose homeostasis, functioning in gluconeogenesis and glycogenolysis. Mutations in this gene cause glycogen storage disease type I (GSD1). This disease, also known as von Gierke disease, is a metabolic disorder characterized by severe hypoglycemia associated with the accumulation of glycogen and fat in the liver and kidneys.[provided by RefSeq, Feb 2011]
- G6PT
- G6PC
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~13.6 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0009287
Submitter: Natera
Inheritance Pattern: AR
Disease ID:MONDO:0009287
Submitter: G2P
Inheritance Pattern: AR
Disease ID:MONDO:0002413
Submitter: ClinGen
Glucose-6-phosphatase (G6Pase) is membrane protein of the endoplasmic reticulum that is composed of a catalytic subunit and transporters for Glucose-6-phosphate, inorganic phosphate, and glucose. The enzyme causes hydrolysis of glucose-6-phosphate (G6P) into glucose during the terminal steps of gluconeogenesis and glycogenolysis (Shieh et al. 2002; Udawat et al. 2019). Glycogen storage disease type Ia (GSD-Ia, MIM232200) also known as von Gierke disease, is caused by deleterious mutations in the *G6PC1* gene. Patients with GSD-Ia experience growth retardation, hypoglycaemia during fasting, and increased serum levels of uric acid, triglycerides, and cholesterol (Wang et al. 2013). The *G6PC1* gene is expressed in the liver, kidney, and intestine, and these are the only organs that release glucose into the blood circulation. G6Pasedeficiency also leads to the accumulation of glucose-6 phosphate (G6P), glycogen, and triglycerides in the liver and kidneys of patients. This results in marked hepatomegaly and nephromegaly. In this curation, 21 variants (missense, nonsense, frameshift), reported in 15 probands in 10 publications (PMID:17607665, 11196115, 11058918, 32436859, 10234610, 10797430, 27139513, 35834487, 8739966, 27511118) are included. GSD-Ia is not more prevalent in any ethnic group, but mutations unique to Caucasian, oriental, and Jewish populations have been described. GSD-Ia patients have been seen to exhibit phenotypic heterogeneity. Among these variants, p.R170X (PMID: 10797430) has been functionally characterized and completely inactivates the G6PC enzyme. The variant p.R83C (PMID:10797430) is identified as the most prevalent mutation in Caucasian and Jewish GSD-Ia patients. In Chinese patients the most prevalent mutations are p.R83H (PMID:324685) and c.648G>T (PMID:10797430). The experimental evidence that support gene-disease relation include biochemical function analysis, functional alteration and animal models (PMID: 12093795, 10738525,8640227, 33359667, 21109326). The study by Ghosh et al., (PMID:12093795), reported the crucial role of His176 in G6Pase catalysis where this His residue in G6Pase becomes phosphorylated generating an enzyme-phosphate intermediate showing that substituting His176 with an Ala residue also completely abolished G6Pase activity, a feature in GSD Ia patients. Functional alteration study was carried out using the hGlc6Pase cDNA cloned in pSVK3 (expression plasmid) which were transfected into COS7 cells. Glc6Pase activity of hGlc6Pase after insertion of the fourpoint mutations which were previously identified in French patients, e.g. W77R, A124T, G184E and L211P were analyzed both in terms of maximal velocity (Vmax) and Glc6P affinity (Km), in comparison with Glc6Pase assayed in microsomes isolated from normal human liver and kidney. None of the four new hGlc6Pase mutants exhibited a Glc6Pase activity higher than that of untransfected COS-7 cells (PMID:107538525). In mouse model study by Mutel et al., G6pc- / mice which were generated by an inducible CRE (CRE ERT2) strategy, demonstrated hyperlipidemia, lactic acidosis, and uricemia, hepatomegaly and steatosis (PMID:21109326). Another mouse model study by Arnaoutova et al., (PMID: 33359667) CRISPR/Cas9-based technology to generate a G6pc-R83C mouse line homozygous for G6PC-p.R83C. It was seen that G6pc-R83C mice were devoid of hepatic and renal G6Pase-α activity and died prematurely, and manifested impaired glucose homeostasis and frequent hypoglycemic seizures, like the symptoms of the global G6pc−/− mice (Lei KJ, 1996)(PMID:8640227), essentially the same pathophysiology as human GSD-Ia patients. In summary, *G6PC1* is definitively associated with autosomal recessive glycogen storage disease Ia and has been repeatedly demonstrated in both the research and clinical diagnosis settings. This classification was approved by the ClinGen General Inborn Errors of Metabolism GCEP on the meeting date [09/27/2024] (SOP Version 10).
Inheritance Pattern: AR
Disease ID:MONDO:0009287
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0009287
Submitter: Myriad Women's Health
Inheritance Pattern: AR
Disease ID:MONDO:0009287
Submitter: PanelApp Australia
Clinical Genomic Database (CGD)
Manifestation: Biochemical; Cardiovascular; Gastrointestinal; Hematologic; Musculoskeletal; Oncologic; Renal
Intervention: Biochemical; Gastrointestinal; Oncologic; Renal
Rationale: Dietary measures (eg, with Glycosade or cornstarch) can be beneficial to allow optimal glucose levels and promote growth and development (additionally, specific carbohydrate sources should be limited); Allopurinol to prevent gout and lipid-lowering medications to prevent hyperlipidemia may be necessary when dietary therapy is ineffective; Citrate supplementation and ACE inhibitors may help prevent development of decrease renal complications, though renal transplant may ultimately be necessary; Surveillance for and treatment of hepatic neoplasms (including liver transplant in some) can be beneficial
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to G6PC1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_000151.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 4 | 163 | 2 | 170 | |
| missense | 18 | 68 | 114 | 8 | 1 | 209 |
| nonsense | 26 | 16 | 2 | 44 | ||
| start loss | 0 | |||||
| frameshift | 24 | 18 | 1 | 43 | ||
| splice donor/acceptor (+/-2bp) | 3 | 8 | 1 | 12 | ||
| Total | 71 | 111 | 122 | 171 | 3 | 478 |
Highest pathogenic variant AF is 0.00039521325
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_000142.2 | 5 | MANE Select | |
| Ensembl | ENSP00000253801.1 | 5 | MANE Select | |
| RefSeq | NP_001257326.1 | 5 | Standard | |
| Ensembl | ENSP00000466202.1 | 4 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- PI3K-Akt signaling pathway - Homo sapiens (human)
- Adipocytokine signaling pathway - Homo sapiens (human)
- Glycolysis / Gluconeogenesis - Homo sapiens (human)
- Insulin resistance - Homo sapiens (human)
- Starch and sucrose metabolism - Homo sapiens (human)
Biological Process
- glycogen metabolic process
- glycogen catabolic process
- gluconeogenesis
- triglyceride metabolic process
- steroid metabolic process
Molecular Function
- glucose-6-phosphatase activity
- phosphotransferase activity, alcohol group as acceptor
- phosphate ion binding
Cellular Component
- endoplasmic reticulum membrane
- integral component of membrane
- integral component of endoplasmic reticulum membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000253801
- Coding exons
- 5
- Length
- 12573
- Individuals with no LoFs
- 125683
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 65
- Defined
- 125748
- p
- 0.000258
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.266 | 182 | 192 | 0.946 | 0.0000109 | 2330 |
| Missense (PolyPhen) | 65 | 71.82 | 0.90504 | 882 | ||
| Synonymous | -1.58 | 100 | 81.8 | 1.22 | 0.00000520 | 715 |
| Loss of Function | 1.54 | 10 | 16.8 | 0.596 | 8.34e-7 | 172 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0.00078 | 0.00078 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00016 | 0.00016 | rare |
| Finnish | 0.000092 | 0.000092 | rare |
| European (Non-Finnish) | 0.00028 | 0.00028 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Hydrolyzes glucose-6-phosphate to glucose in the endoplasmic reticulum. Forms with the glucose-6-phosphate transporter (SLC37A4/G6PT) the complex responsible for glucose production through glycogenolysis and gluconeogenesis. Hence, it is the key enzyme in homeostatic regulation of blood glucose levels.;
- Disease
- DISEASE: Glycogen storage disease 1A (GSD1A) [MIM:232200]: A metabolic disorder characterized by impairment of terminal steps of glycogenolysis and gluconeogenesis. Patients manifest a wide range of clinical symptoms and biochemical abnormalities, including hypoglycemia, severe hepatomegaly due to excessive accumulation of glycogen, kidney enlargement, growth retardation, lactic acidemia, hyperlipidemia, and hyperuricemia. {ECO:0000269|PubMed:10070617, ECO:0000269|PubMed:10094563, ECO:0000269|PubMed:10447271, ECO:0000269|PubMed:10612834, ECO:0000269|PubMed:10738005, ECO:0000269|PubMed:10748407, ECO:0000269|PubMed:10874313, ECO:0000269|PubMed:10960498, ECO:0000269|PubMed:11058903, ECO:0000269|PubMed:11058910, ECO:0000269|PubMed:12373566, ECO:0000269|PubMed:15151508, ECO:0000269|PubMed:15316959, ECO:0000269|PubMed:15542400, ECO:0000269|PubMed:7573034, ECO:0000269|PubMed:7623438, ECO:0000269|PubMed:7655466, ECO:0000269|PubMed:8182131, ECO:0000269|PubMed:8733042, ECO:0000269|PubMed:9001800, ECO:0000269|PubMed:9332655, ECO:0000269|PubMed:9506659, ECO:0000269|PubMed:9700612, ECO:0000269|PubMed:9700613}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.795
Intolerance Scores
- RVIS EVS
- -0.74
- RVIS percentile EVS
- 13.94
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.961
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |