GBP1

guanylate binding protein 1, the group of Guanylate binding proteins

Basic information

Region (hg38): 1:89051882-89065360

Links

ENSG00000117228 ∙ NCBI:2633 ∙ OMIM:600411 ∙ HGNC:4182 ∙ Uniprot:P32455 ∙ 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 GBP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GBP1 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			46	7		53
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	46	9	0

Variants in GBP1

This is a list of pathogenic ClinVar variants found in the GBP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-89053377-C-T		not specified	Uncertain significance (Jun 17, 2024)
1-89053386-A-G		not specified	Uncertain significance (Jun 16, 2023)
1-89053413-T-G		not specified	Uncertain significance (Jun 18, 2021)
1-89053459-G-T		not specified	Uncertain significance (Sep 03, 2024)
1-89054646-GAAAAAC-G		Neutrophil inclusion bodies	Likely pathogenic (-)
1-89054701-G-T		not specified	Uncertain significance (Jun 16, 2024)
1-89054717-T-C		not specified	Likely benign (Aug 13, 2021)
1-89054722-A-G			Likely benign (Jan 01, 2025)
1-89054737-T-C		not specified	Uncertain significance (Jun 11, 2024)
1-89054824-T-C		not specified	Uncertain significance (May 06, 2022)
1-89054831-A-C		not specified	Uncertain significance (Jul 02, 2024)
1-89054855-A-T		not specified	Uncertain significance (Jan 29, 2024)
1-89055205-A-G		not specified	Uncertain significance (Aug 10, 2021)
1-89056021-T-C		not specified	Uncertain significance (Aug 15, 2023)
1-89056045-A-G		not specified	Uncertain significance (Aug 04, 2024)
1-89056075-C-T		not specified	Likely benign (Jan 10, 2022)
1-89056089-C-T		not specified	Uncertain significance (Apr 28, 2022)
1-89056090-C-G		not specified	Uncertain significance (Jun 24, 2022)
1-89056155-A-G		not specified	Uncertain significance (Jan 19, 2024)
1-89056209-C-T		not specified	Uncertain significance (Mar 14, 2024)
1-89056212-T-C		not specified	Uncertain significance (Mar 06, 2023)
1-89056217-T-G		not specified	Likely benign (Jan 17, 2023)
1-89056855-G-A		not specified	Uncertain significance (Feb 27, 2023)
1-89056936-C-G		not specified	Uncertain significance (Mar 27, 2023)
1-89057000-G-C		not specified	Uncertain significance (Mar 21, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GBP1	protein_coding	protein_coding	ENST00000370473	10	13042

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.26e-15	0.0423	125417	1	330	125748	0.00132

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.452	338	315	1.07	0.0000170	3898
Missense in Polyphen		137	137.69	0.99497		1832
Synonymous	-1.05	137	122	1.12	0.00000683	1096
Loss of Function	0.608	25	28.5	0.877	0.00000149	333

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00538	0.00538
Ashkenazi Jewish	0.00	0.00
East Asian	0.00652	0.00644
Finnish	0.000185	0.000185
European (Non-Finnish)	0.000722	0.000703
Middle Eastern	0.00652	0.00644
South Asian	0.000163	0.000163
Other	0.000653	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Hydrolyzes GTP to GMP in 2 consecutive cleavage reactions. Exhibits antiviral activity against influenza virus. Promote oxidative killing and deliver antimicrobial peptides to autophagolysosomes, providing broad host protection against different pathogen classes. {ECO:0000269|PubMed:22106366}.
• Pathway: NOD-like receptor signaling pathway - Homo sapiens (human);Type II interferon signaling (IFNG);Cytokine Signaling in Immune system;Immune System;Interferon gamma signaling;Interferon Signaling (Consensus)

Recessive Scores

• pRec: 0.173

Intolerance Scores

• loftool: 0.958
• rvis_EVS: -0.08
• rvis_percentile_EVS: 47.2

Haploinsufficiency Scores

• pHI: 0.514
• hipred: N
• hipred_score: 0.252
• ghis: 0.384

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.287

Gene Damage Prediction

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

Gene ontology

• Biological process: regulation of calcium-mediated signaling;negative regulation of T cell receptor signaling pathway;protein homooligomerization;defense response to virus;interferon-gamma-mediated signaling pathway;negative regulation of ERK1 and ERK2 cascade;cellular response to interferon-gamma;cellular response to interleukin-1;cellular response to tumor necrosis factor;protein localization to vacuole;negative regulation of substrate adhesion-dependent cell spreading;negative regulation of interleukin-2 secretion;regulation of protein localization to plasma membrane;negative regulation of protein localization to plasma membrane
• Cellular component: Golgi membrane;extracellular region;cytoplasm;Golgi apparatus;cytosol;plasma membrane;vesicle membrane;actin cytoskeleton
• Molecular function: actin binding;GTPase activity;protein binding;GTP binding;GDP binding;enzyme binding;cytokine binding;spectrin binding;identical protein binding;protein homodimerization activity;Hsp90 protein binding