GBP5

guanylate binding protein 5, the group of Guanylate binding proteins

Basic information

Region (hg38): 1:89256189-89272860

Links

ENSG00000154451 ∙ NCBI:115362 ∙ OMIM:611467 ∙ HGNC:19895 ∙ Uniprot:Q96PP8 ∙ 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 GBP5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GBP5 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				1		1
missense			39	3	2	44
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	40	4	2

Variants in GBP5

This is a list of pathogenic ClinVar variants found in the GBP5 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-89260715-C-T		not specified	Likely benign (Dec 07, 2021)
1-89260720-G-A			Uncertain significance (-)
1-89260726-T-C		not specified	Uncertain significance (Dec 14, 2021)
1-89260728-G-A			Likely benign (Jul 01, 2022)
1-89262285-G-C		not specified	Uncertain significance (Jan 30, 2024)
1-89262325-C-T		not specified	Uncertain significance (Jan 19, 2024)
1-89262327-T-C		not specified	Uncertain significance (Jan 24, 2025)
1-89262353-G-A		not specified	Uncertain significance (May 08, 2023)
1-89262358-C-G		not specified	Uncertain significance (Jan 27, 2025)
1-89262371-G-A		not specified	Uncertain significance (Feb 07, 2025)
1-89262693-T-G		not specified	Uncertain significance (Apr 07, 2023)
1-89262700-G-A		not specified	Uncertain significance (Feb 13, 2024)
1-89262706-G-T		not specified	Uncertain significance (Mar 30, 2024)
1-89262724-T-G		not specified	Uncertain significance (Feb 28, 2023)
1-89262745-G-C		not specified	Uncertain significance (Nov 27, 2024)
1-89263746-T-C		not specified	Uncertain significance (Jul 12, 2023)
1-89263756-C-T		not specified	Uncertain significance (Dec 16, 2022)
1-89263759-G-A		not specified	Uncertain significance (May 13, 2024)
1-89263795-T-C		not specified	Uncertain significance (Mar 29, 2024)
1-89263854-G-A		not specified	Uncertain significance (Aug 23, 2021)
1-89263911-C-T		not specified	Likely benign (May 27, 2022)
1-89264687-T-G		not specified	Uncertain significance (Jan 28, 2025)
1-89264717-T-G		not specified	Uncertain significance (Mar 18, 2024)
1-89264835-C-T		not specified	Uncertain significance (Oct 07, 2024)
1-89264847-T-C		not specified	Uncertain significance (Aug 28, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GBP5	protein_coding	protein_coding	ENST00000343435	10	13912

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.11e-10	0.704	125616	0	132	125748	0.000525

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.304	320	305	1.05	0.0000150	3888
Missense in Polyphen		74	77.622	0.95334		1054
Synonymous	-0.488	126	119	1.06	0.00000642	1085
Loss of Function	1.44	18	25.9	0.695	0.00000120	319

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00637	0.00446
Ashkenazi Jewish	0.00	0.00
East Asian	0.000272	0.000272
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000124	0.000123
Middle Eastern	0.000272	0.000272
South Asian	0.000294	0.000294
Other	0.000489	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: As an activator of NLRP3 inflammasome assembly, plays a role in innate immunity and inflammation. Promotes selective NLRP3 inflammasome assembly in response to microbial and soluble, but not crystalline, agents (PubMed:22461501). Hydrolyzes GTP, but in contrast to other family members, does not produce GMP (PubMed:20180847). {ECO:0000269|PubMed:20180847, ECO:0000269|PubMed:22461501}.
• Pathway: NOD-like receptor signaling pathway - Homo sapiens (human);Cytokine Signaling in Immune system;Immune System;Interferon gamma signaling;Interferon Signaling (Consensus)

Intolerance Scores

• loftool: 0.969
• rvis_EVS: 0.53
• rvis_percentile_EVS: 81.01

Haploinsufficiency Scores

• pHI: 0.0560
• hipred: N
• hipred_score: 0.132
• ghis: 0.444

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0102

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gbp5
• Phenotype: immune system phenotype; hematopoietic system phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: inflammatory response;response to bacterium;protein localization to Golgi apparatus;positive regulation of innate immune response;interleukin-1 beta secretion;protein homotetramerization;cellular response to interferon-gamma;interleukin-18 secretion;positive regulation of cytokine production involved in inflammatory response;positive regulation of NLRP3 inflammasome complex assembly
• Cellular component: Golgi membrane;cytoplasm;Golgi apparatus;membrane;cytoplasmic vesicle;perinuclear region of cytoplasm
• Molecular function: GTPase activity;protein binding;GTP binding;identical protein binding;protein homodimerization activity