GBP4

guanylate binding protein 4, the group of Guanylate binding proteins

Basic information

Region (hg38): 1:89181143-89198942

Links

ENSG00000162654 ∙ NCBI:115361 ∙ OMIM:612466 ∙ HGNC:20480 ∙ Uniprot:Q96PP9 ∙ 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 GBP4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GBP4 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	1	4
missense			28	1		29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	28	4	1

Variants in GBP4

This is a list of pathogenic ClinVar variants found in the GBP4 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-89185298-T-G		not specified	Uncertain significance (Jun 11, 2024)
1-89185356-G-A			Likely benign (Mar 01, 2023)
1-89185389-T-G		not specified	Uncertain significance (Jun 17, 2024)
1-89185450-T-C		not specified	Uncertain significance (Apr 06, 2024)
1-89186446-C-G		not specified	Uncertain significance (May 18, 2023)
1-89187044-A-G		not specified	Uncertain significance (Oct 26, 2021)
1-89188681-C-G		not specified	Uncertain significance (Jan 31, 2024)
1-89188694-G-A		not specified	Uncertain significance (Aug 22, 2023)
1-89188744-T-C			Likely benign (Jan 01, 2023)
1-89188745-G-A		not specified	Uncertain significance (Nov 09, 2023)
1-89188787-A-G		not specified	Uncertain significance (Sep 22, 2021)
1-89190051-T-C		not specified	Uncertain significance (Oct 12, 2021)
1-89190127-C-T		not specified	Uncertain significance (Feb 15, 2023)
1-89190172-G-C		not specified	Uncertain significance (Mar 20, 2024)
1-89190183-T-G		not specified	Uncertain significance (Feb 17, 2023)
1-89190197-G-A			Likely benign (Jun 01, 2022)
1-89190219-G-A		not specified	Uncertain significance (Apr 18, 2023)
1-89190228-A-G		not specified	Uncertain significance (Jun 30, 2022)
1-89190231-T-C		not specified	Uncertain significance (Aug 16, 2021)
1-89190261-C-G		not specified	Uncertain significance (Jan 24, 2023)
1-89191291-G-A			Benign (Jun 20, 2018)
1-89191326-C-G		not specified	Uncertain significance (Jul 05, 2023)
1-89191332-T-C		not specified	Uncertain significance (Jan 09, 2024)
1-89191420-G-A		not specified	Uncertain significance (Apr 15, 2024)
1-89191440-C-T		not specified	Uncertain significance (Dec 03, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GBP4	protein_coding	protein_coding	ENST00000355754	11	17785

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.18e-16	0.0352	124807	10	931	125748	0.00375

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.481	318	343	0.927	0.0000176	4219
Missense in Polyphen		82	95.696	0.85688		1357
Synonymous	0.0416	129	130	0.995	0.00000689	1193
Loss of Function	0.550	25	28.2	0.888	0.00000138	344

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00396	0.00396
Ashkenazi Jewish	0.00206	0.00199
East Asian	0.000490	0.000489
Finnish	0.00126	0.00125
European (Non-Finnish)	0.00571	0.00559
Middle Eastern	0.000490	0.000489
South Asian	0.00384	0.00370
Other	0.00348	0.00343

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds GTP, GDP and GMP. Hydrolyzes GTP very efficiently; GDP rather than GMP is the major reaction product. Plays a role in erythroid differentiation (By similarity). {ECO:0000250}.
• 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: 0.953
• rvis_EVS: 1.76
• rvis_percentile_EVS: 96.73

Haploinsufficiency Scores

• pHI: 0.0605
• hipred: N
• hipred_score: 0.112
• ghis: 0.404

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.255

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gbp3

Gene ontology

• Biological process: cellular response to interferon-gamma
• Cellular component: Golgi membrane;nucleus;cytosol;perinuclear region of cytoplasm
• Molecular function: GTPase activity;protein binding;GTP binding;protein homodimerization activity