GBP3

protein-coding

guanylate binding protein 3, the group of Guanylate binding proteins

Gene summary

This gene encodes a member of the guanylate-binding protein (GBP) family. GBPs specifically bind guanine nucleotides (GMP, GDP, and GTP) and contain two of the three consensus motifs found in typical GTP-binding proteins. The encoded protein interacts with a member of the germinal center kinase family. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2017]

MANE transcript

NM_018284.3

Inheritance

—

ClinVar variants

U:88B:9

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.98

Max pathogenic AF

—

Genomic locus

chr1:89,006,666-89,022,894

External References & Databases

Ensembl (ENSG00000117226)

Transcript & Mutation Effects

hg38 • Region Span ~16.2 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 GBP3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 84

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018284.3. 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						0
missense			79 clinvar	8 clinvar	1 clinvar	88
nonsense			1 clinvar			1
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			7 clinvar			7
Total	0	0	88	8	1	97

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 31 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_018284.3	RefSeq	NP_060754.2	10	MANE Select
ENST00000370481.9	Ensembl	ENSP00000359512.4	10	MANE Select
NM_001319179.2	RefSeq	NP_001306108.1	9	Standard
NM_001319180.2	RefSeq	NP_001306109.1	8	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
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

Biological Process

defense response to virus
cellular response to interleukin-1
cellular response to tumor necrosis factor

Molecular Function

GTPase activity
protein binding
GTP binding
protein homodimerization activity

Cellular Component

Golgi membrane
cytoplasm
cytosol
perinuclear region of cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000370481
Coding exons: 10
Length: 16229
Individuals with no LoFs: 125184
Homozygous LoFs: 28
Heterozygous LoFs: 536
Defined: 125748
p: 0.00225

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.0375	305	303	1.01	0.0000152	3912
Missense (PolyPhen)		64	72.904	0.87787		1019
Synonymous	0.740	108	118	0.913	0.00000621	1105
Loss of Function	0.109	28	28.6	0.978	0.00000156	335

Population LoF Frequency

Population	CAF	p-value	Status
African	0.030	0.028	notable
Latino/Admixed American	0.0014	0.0013	notable
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00022	0.00022	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00049	0.00043	rare
South Asian	0.00030	0.00029	rare
Other	0.0012	0.00098	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Exhibits antiviral activity against influenza virus. {ECO:0000269|PubMed:22106366}.;

Recessive Scores

pRec: 0.0819

Intolerance Scores

LoFtool: 0.899
RVIS EVS: 3.02
RVIS percentile EVS: 99.23

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.435

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High