GBP4

protein-coding

guanylate binding protein 4, the group of Guanylate binding proteins

Gene summary

Guanylate-binding proteins, such as GBP4, are induced by interferon and hydrolyze GTP to both GDP and GMP (Vestal, 2005 [PubMed 16108726]).[supplied by OMIM, Dec 2008]

MANE transcript

NM_052941.5

Inheritance

—

ClinVar variants

U:98B:11

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.89

Max pathogenic AF

—

Genomic locus

chr1:89,181,144-89,198,942

External References & Databases

Ensembl (ENSG00000162654)

Transcript & Mutation Effects

hg38 • Region Span ~17.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to GBP4 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 92

not providedTotal: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_052941.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	4 clinvar	1 clinvar	6
missense			91 clinvar	6 clinvar		97
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			6 clinvar			6
Total	0	0	98	10	1	109

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 6 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_052941.5	RefSeq	NP_443173.2	11	MANE Select
ENST00000355754.7	Ensembl	ENSP00000359490.5	11	MANE Select
ENST00000953047.1	Ensembl	ENSP00000623106.1	10	Standard
ENST00000953047.2	Ensembl	ENSP00000623106.1	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

NOD-like receptor signaling pathway - Homo sapiens (human)
Cytokine Signaling in Immune system
Immune System
Interferon gamma signaling
Interferon Signaling

Biological Process

cellular response to interferon-gamma

Molecular Function

GTPase activity
protein binding
GTP binding
protein homodimerization activity

Cellular Component

Golgi membrane
nucleus
cytosol
perinuclear region of cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000355754
Coding exons: 11
Length: 17785
Individuals with no LoFs: 124807
Homozygous LoFs: 10
Heterozygous LoFs: 931
Defined: 125748
p: 0.00375

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.481	318	343	0.927	0.0000176	4219
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00099	0.00098	rare
Latino/Admixed American	0.0030	0.0029	notable
Ashkenazi Jewish	0.0021	0.0020	notable
East Asian	0.00049	0.00049	rare
Finnish	0.0013	0.0012	notable
European (Non-Finnish)	0.0057	0.0056	notable
South Asian	0.0038	0.0037	notable
Other	0.0035	0.0034	notable

dbNSFP Gene Annotations

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}.;

Intolerance Scores

LoFtool: 0.953
RVIS EVS: 1.76
RVIS percentile EVS: 96.73

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.255

Gene Damage Prediction

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