GBP1

guanylate binding protein 1, the group of Guanylate binding proteins

Basic information

Region (hg38): 1:89051882-89065360

Links

ENSG00000117228

∙ NCBI:2633 ∙ OMIM:600411 ∙ HGNC:4182 ∙ Uniprot:P32455 ∙ 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 GBP1 gene.

not_specified (83 variants)
not_provided (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GBP1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000002053.3. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				2 clinvar		2
missense			73 clinvar	13 clinvar		86
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	73	15	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GBP1	protein_coding	protein_coding	ENST00000370473	10	13042

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.26e-15	0.0423	125417	1	330	125748	0.00132

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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00538	0.00538
Ashkenazi Jewish	0.00	0.00
East Asian	0.00652	0.00644
Finnish	0.000185	0.000185
European (Non-Finnish)	0.000722	0.000703
Middle Eastern	0.00652	0.00644
South Asian	0.000163	0.000163
Other	0.000653	0.000652

dbNSFP

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}.;
Pathway: NOD-like receptor signaling pathway - Homo sapiens (human);Type II interferon signaling (IFNG);Cytokine Signaling in Immune system;Immune System;Interferon gamma signaling;Interferon Signaling (Consensus)

Recessive Scores

pRec: 0.173

Intolerance Scores

loftool: 0.958
rvis_EVS: -0.08
rvis_percentile_EVS: 47.2

Haploinsufficiency Scores

pHI: 0.514
hipred: N
hipred_score: 0.252
ghis: 0.384

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.287

Gene Damage Prediction

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

Gene ontology

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;negative regulation of ERK1 and ERK2 cascade;cellular response to interferon-gamma;cellular response to interleukin-1;cellular response to tumor necrosis factor;protein localization to vacuole;negative regulation of substrate adhesion-dependent cell spreading;negative regulation of interleukin-2 secretion;regulation of protein localization to plasma membrane;negative regulation of protein localization to plasma membrane
Cellular component: Golgi membrane;extracellular region;cytoplasm;Golgi apparatus;cytosol;plasma membrane;vesicle membrane;actin cytoskeleton
Molecular function: actin binding;GTPase activity;protein binding;GTP binding;GDP binding;enzyme binding;cytokine binding;spectrin binding;identical protein binding;protein homodimerization activity;Hsp90 protein binding