GBP2

guanylate binding protein 2, the group of Guanylate binding proteins

Basic information

Region (hg38): 1:89106132-89150456

Links

ENSG00000162645 ∙ NCBI:2634 ∙ OMIM:600412 ∙ HGNC:4183 ∙ Uniprot:P32456 ∙ 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 GBP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GBP2 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				3		3
missense			39	1		40
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	39	4	0

Variants in GBP2

This is a list of pathogenic ClinVar variants found in the GBP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-89108192-T-C		not specified	Uncertain significance (Aug 01, 2024)
1-89108195-G-A		not specified	Uncertain significance (Aug 15, 2023)
1-89108225-C-T		not specified	Uncertain significance (Sep 20, 2023)
1-89108281-C-T		not specified	Uncertain significance (Dec 10, 2024)
1-89108282-G-A		not specified	Uncertain significance (Jun 28, 2024)
1-89109698-C-G		not specified	Uncertain significance (Dec 07, 2024)
1-89109713-C-T		not specified	Uncertain significance (Oct 16, 2024)
1-89110206-G-T		not specified	Uncertain significance (Apr 22, 2022)
1-89110232-T-A		not specified	Uncertain significance (Jan 14, 2025)
1-89110251-T-G		not specified	Uncertain significance (May 30, 2023)
1-89112476-A-T		not specified	Uncertain significance (Dec 20, 2024)
1-89112539-C-T		not specified	Uncertain significance (Jun 21, 2023)
1-89112557-G-A		not specified	Uncertain significance (Dec 13, 2022)
1-89112582-C-G		not specified	Uncertain significance (Dec 06, 2024)
1-89114002-A-G		Inherited susceptibility to mycobacterial diseases	Likely risk allele (-)
1-89114024-T-C		not specified	Likely benign (Oct 14, 2021)
1-89114066-T-C		not specified	Uncertain significance (Feb 21, 2024)
1-89114098-C-A		not specified	Uncertain significance (Nov 13, 2024)
1-89114149-T-C		not specified	Uncertain significance (Nov 09, 2024)
1-89114165-C-T		not specified	Uncertain significance (May 03, 2023)
1-89114173-G-T		not specified	Uncertain significance (Feb 21, 2025)
1-89114192-C-T		not specified	Uncertain significance (Jan 08, 2024)
1-89114228-C-A		not specified	Uncertain significance (Nov 15, 2024)
1-89114266-T-C		not specified	Uncertain significance (Jan 26, 2025)
1-89117015-C-T		not specified	Uncertain significance (Sep 17, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GBP2	protein_coding	protein_coding	ENST00000370466	10	44325

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.03e-10	0.786	125672	0	76	125748	0.000302

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.107	312	317	0.983	0.0000162	3918
Missense in Polyphen		85	95.611	0.88902		1251
Synonymous	-0.112	123	121	1.01	0.00000664	1084
Loss of Function	1.60	19	28.1	0.675	0.00000153	321

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000355	0.000355
Ashkenazi Jewish	0.00	0.00
East Asian	0.000272	0.000272
Finnish	0.000185	0.000185
European (Non-Finnish)	0.000291	0.000290
Middle Eastern	0.000272	0.000272
South Asian	0.000754	0.000752
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Hydrolyzes GTP to GMP in 2 consecutive cleavage reactions, but the major reaction product is GDP (PubMed:8706832). Exhibits antiviral activity against influenza virus. Promote oxidative killing and deliver antimicrobial peptides to autophagolysosomes, providing broad host protection against different pathogen classes (By similarity). {ECO:0000250|UniProtKB:P32455, ECO:0000269|PubMed:8706832}.
• Pathway: NOD-like receptor signaling pathway - Homo sapiens (human);Cytokine Signaling in Immune system;Immune System;Interferon gamma signaling;Interferon alpha/beta signaling;Interferon Signaling (Consensus)

Intolerance Scores

• loftool: 0.875
• rvis_EVS: 0.96
• rvis_percentile_EVS: 90.15

Haploinsufficiency Scores

• pHI: 0.155
• hipred: N
• hipred_score: 0.290
• ghis: 0.442

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.945

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gbp2
• Phenotype: immune system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: immune response;protein localization to nucleus;interferon-gamma-mediated signaling pathway;type I interferon signaling pathway;cellular response to interferon-gamma;cellular response to interleukin-1;cellular response to tumor necrosis factor
• Cellular component: Golgi membrane;nucleus;nucleoplasm;cytoplasm;Golgi apparatus;cytosol;actin cytoskeleton;perinuclear region of cytoplasm
• Molecular function: GTPase activity;protein binding;GTP binding;protein homodimerization activity