GBP1

protein-coding

guanylate binding protein 1, the group of Guanylate binding proteins

Gene summary

Guanylate binding protein expression is induced by interferon. Guanylate binding proteins are characterized by their ability to specifically bind guanine nucleotides (GMP, GDP, and GTP) and are distinguished from the GTP-binding proteins by the presence of 2 binding motifs rather than 3. [provided by RefSeq, Jul 2008]

MANE transcript

NM_002053.3

Inheritance

—

ClinVar variants

U:90B:15

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.88

Max pathogenic AF

—

Genomic locus

chr1:89,051,882-89,065,360

External References & Databases

Ensembl (ENSG00000117228)

Transcript & Mutation Effects

hg38 • Region Span ~13.5 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 GBP1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 91

not providedTotal: 6

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_002053.3. 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	2 clinvar		3
missense			84 clinvar	13 clinvar		97
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	0	90	15	0	105

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 21 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_002053.3	RefSeq	NP_002044.2	10	MANE Select
ENST00000370473.5	Ensembl	ENSP00000359504.4	10	MANE Select
ENST00000681280.1	Ensembl	ENSP00000506404.1	5	Standard
ENST00000872735.1	Ensembl	ENSP00000542794.1	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)
Type II interferon signaling (IFNG)
Cytokine Signaling in Immune system
Immune System
Interferon gamma signaling

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

Molecular Function

actin binding
GTPase activity
protein binding
GTP binding
GDP binding

Cellular Component

Golgi membrane
extracellular region
cytoplasm
Golgi apparatus
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000370473
Coding exons: 10
Length: 13042
Individuals with no LoFs: 125417
Homozygous LoFs: 1
Heterozygous LoFs: 330
Defined: 125748
p: 0.00132

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.452	338	315	1.07	0.0000170	3898
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0035	0.0035	notable
Latino/Admixed American	0.0019	0.0018	notable
Ashkenazi Jewish	0	0.0	absent
East Asian	0.0065	0.0064	notable
Finnish	0.00018	0.00018	rare
European (Non-Finnish)	0.00072	0.00070	rare
South Asian	0.00016	0.00016	rare
Other	0.00065	0.00065	rare

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.173

Intolerance Scores

LoFtool: 0.958
RVIS EVS: -0.08
RVIS percentile EVS: 47.2

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.287

Gene Damage Prediction

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