GBP3

guanylate binding protein 3, the group of Guanylate binding proteins

Basic information

Region (hg38): 1:89006666-89022894

Links

ENSG00000117226 ∙ NCBI:2635 ∙ OMIM:600413 ∙ HGNC:4184 ∙ Uniprot:Q9H0R5 ∙ 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 GBP3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GBP3 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						0
missense			25	3	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	25	3	1

Variants in GBP3

This is a list of pathogenic ClinVar variants found in the GBP3 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-89007764-T-A		not specified	Uncertain significance (Dec 03, 2021)
1-89007770-A-G			Benign (May 01, 2023)
1-89007842-C-A		not specified	Uncertain significance (Feb 05, 2024)
1-89009008-A-G		not specified	Uncertain significance (Oct 21, 2024)
1-89009043-A-T		not specified	Uncertain significance (Dec 14, 2023)
1-89009055-C-G		not specified	Uncertain significance (Dec 20, 2021)
1-89009134-C-T		not specified	Uncertain significance (Dec 16, 2022)
1-89009449-T-C		not specified	Uncertain significance (Dec 05, 2024)
1-89009454-G-A		not specified	Uncertain significance (Sep 09, 2024)
1-89010998-C-T		not specified	Uncertain significance (Jun 18, 2021)
1-89011105-G-T		not specified	Likely benign (Oct 03, 2022)
1-89011778-T-A		not specified	Uncertain significance (Oct 24, 2024)
1-89011887-T-C		not specified	Uncertain significance (Jan 31, 2024)
1-89011923-C-T		not specified	Uncertain significance (May 09, 2023)
1-89011928-G-A		not specified	Uncertain significance (Nov 22, 2023)
1-89011936-T-C		not specified	Uncertain significance (Mar 21, 2023)
1-89011965-C-T		not specified	Uncertain significance (Mar 11, 2022)
1-89012007-T-C		not specified	Uncertain significance (Oct 30, 2024)
1-89013259-G-A		not specified	Uncertain significance (May 26, 2022)
1-89013296-C-G		not specified	Uncertain significance (Oct 20, 2023)
1-89013317-C-T		not specified	Uncertain significance (Jun 16, 2024)
1-89013328-C-T		not specified	Uncertain significance (Nov 20, 2024)
1-89013329-G-A		not specified	Likely benign (Aug 02, 2021)
1-89013343-T-C		not specified	Uncertain significance (May 09, 2023)
1-89013379-C-T		not specified	Likely benign (Dec 05, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GBP3	protein_coding	protein_coding	ENST00000370481	10	16229

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.03e-18	0.00466	125184	28	536	125748	0.00225

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0375	305	303	1.01	0.0000152	3912
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0310	0.0296
Ashkenazi Jewish	0.00	0.00
East Asian	0.000217	0.000217
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000494	0.000431
Middle Eastern	0.000217	0.000217
South Asian	0.000302	0.000294
Other	0.00120	0.000978

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Exhibits antiviral activity against influenza virus. {ECO:0000269|PubMed:22106366}.
• Pathway: 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;Interferon Signaling (Consensus)

Recessive Scores

• pRec: 0.0819

Intolerance Scores

• loftool: 0.899
• rvis_EVS: 3.02
• rvis_percentile_EVS: 99.23

Haploinsufficiency Scores

• pHI: 0.0601
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.435

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gbp2b
• Phenotype: growth/size/body region phenotype; hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); immune system phenotype; digestive/alimentary phenotype

Gene ontology

• Biological process: defense response to virus;cellular response to interleukin-1;cellular response to tumor necrosis factor
• Cellular component: Golgi membrane;cytoplasm;cytosol;perinuclear region of cytoplasm
• Molecular function: GTPase activity;protein binding;GTP binding;protein homodimerization activity