G6PC2

glucose-6-phosphatase catalytic subunit 2, the group of Glucose 6-phosphatases, catalytic

Basic information

Region (hg38): 2:168901291-168910000

Links

ENSG00000152254 ∙ NCBI:57818 ∙ OMIM:608058 ∙ HGNC:28906 ∙ Uniprot:Q9NQR9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the G6PC2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the G6PC2 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2		2
missense			13		2	15
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	14	2	2

Variants in G6PC2

This is a list of pathogenic ClinVar variants found in the G6PC2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
2-168901350-A-G		not specified	Uncertain significance (Jul 07, 2022)
2-168901489-T-C		not specified	Uncertain significance (Aug 11, 2022)
2-168902447-T-A		not specified	Uncertain significance (Jan 30, 2024)
2-168904601-C-G		not specified	Uncertain significance (Nov 12, 2021)
2-168904613-A-G		not specified	Uncertain significance (Jan 03, 2024)
2-168906660-G-A		G6PC2-related disorder	Benign (May 28, 2019)
2-168906692-T-C		not specified	Uncertain significance (May 21, 2024)
2-168906712-T-G		not specified	Uncertain significance (Jan 03, 2024)
2-168907579-G-T		not specified	Uncertain significance (Jan 31, 2022)
2-168907638-G-A		G6PC2-related disorder	Likely benign (Apr 01, 2019)
2-168907710-G-A		G6PC2-related disorder	Likely benign (Apr 02, 2019)
2-168907858-C-T		Fasting plasma glucose level quantitative trait locus 1	Uncertain significance (Mar 05, 2018)
2-168907884-C-A		not specified	Uncertain significance (Jan 31, 2022)
2-168907898-G-A		not specified	Uncertain significance (May 12, 2024)
2-168907957-G-A		not specified	Uncertain significance (Jun 08, 2022)
2-168907972-T-G		not specified	Uncertain significance (Nov 22, 2023)
2-168907979-T-A		not specified	Uncertain significance (Jul 14, 2021)
2-168907981-T-C		G6PC2-related disorder	Benign (Apr 01, 2019)
2-168908036-C-G		G6PC2-related disorder	Benign (Oct 24, 2019)
2-168908041-C-G		not specified	Uncertain significance (Dec 13, 2022)
2-168908046-G-A		not specified	Uncertain significance (Mar 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
G6PC2	protein_coding	protein_coding	ENST00000375363	5	8756

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.96e-16	0.00133	125242	2	504	125748	0.00201

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.237	194	185	1.05	0.00000937	2339
Missense in Polyphen		61	56.01	1.0891		759
Synonymous	-1.84	90	70.4	1.28	0.00000393	689
Loss of Function	-1.09	21	16.2	1.29	8.57e-7	166

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00337	0.00337
Ashkenazi Jewish	0.00377	0.00378
East Asian	0.000326	0.000326
Finnish	0.000139	0.000139
European (Non-Finnish)	0.00279	0.00278
Middle Eastern	0.000326	0.000326
South Asian	0.00101	0.00101
Other	0.00326	0.00326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May hydrolyze glucose-6-phosphate to glucose in the endoplasmic reticulum. May be responsible for glucose production through glycogenolysis and gluconeogenesis (By similarity). {ECO:0000250}.
• Pathway: 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);Carbohydrate digestion and absorption - Homo sapiens (human);FoxO signaling pathway - Homo sapiens (human);AMPK signaling pathway - Homo sapiens (human);Glucagon signaling pathway - Homo sapiens (human);Galactose metabolism - Homo sapiens (human);Insulin signaling pathway - Homo sapiens (human);Amino Acid metabolism;PI3K-Akt Signaling Pathway;Metabolism of carbohydrates;glycogenolysis;Metabolism;gluconeogenesis;Gluconeogenesis;Glucose metabolism (Consensus)

Recessive Scores

• pRec: 0.154

Intolerance Scores

• loftool: 0.623
• rvis_EVS: 0.69
• rvis_percentile_EVS: 85.18

Haploinsufficiency Scores

• pHI: 0.130
• hipred: N
• hipred_score: 0.250
• ghis: 0.460

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.633

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	Medium	Medium
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: G6pc2
• Phenotype: hematopoietic system phenotype; immune system phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: gluconeogenesis;dephosphorylation;glucose homeostasis;regulation of insulin secretion;glucose 6-phosphate metabolic process
• Cellular component: endoplasmic reticulum membrane;integral component of membrane
• Molecular function: glucose-6-phosphatase activity