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.

not_specified (73 variants)
not_provided (4 variants)
Inherited_susceptibility_to_mycobacterial_diseases (1 variants)

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. These statistics are base on transcript: NM_000004120.5. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	3 clinvar		4
missense			69 clinvar	4 clinvar		73
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	70	7	0

Loading clinvar variants...

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