G3BP1

G3BP stress granule assembly factor 1, the group of RNA binding motif containing|Endoribonucleases

Basic information

Region (hg38): 5:151771045-151812911

Links

ENSG00000145907 ∙ NCBI:10146 ∙ OMIM:608431 ∙ HGNC:30292 ∙ Uniprot:Q13283 ∙ 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 G3BP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the G3BP1 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			28			28
nonsense			1			1
start loss						0
frameshift			2			2
inframe indel						0
splice donor/acceptor (+/-2bp)			2			2
splice region			1			1
non coding		1				1
Total	0	1	33	0	0

Variants in G3BP1

This is a list of pathogenic ClinVar variants found in the G3BP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-151786705-A-G		not specified	Uncertain significance (Nov 10, 2024)
5-151786716-G-A			Likely pathogenic (May 13, 2025)
5-151790394-A-G			Uncertain significance (Oct 18, 2023)
5-151790959-A-T			Uncertain significance (Jun 02, 2024)
5-151790974-A-G		not specified	Uncertain significance (Sep 01, 2024)
5-151790995-T-C		not specified	Uncertain significance (Aug 28, 2024)
5-151791054-G-C		not specified	Uncertain significance (Jun 17, 2022)
5-151791058-C-T			Uncertain significance (Dec 29, 2023)
5-151794168-G-A		not specified	Uncertain significance (Nov 03, 2023)
5-151794193-A-G		not specified	Uncertain significance (Feb 25, 2025)
5-151794196-T-C			Uncertain significance (Oct 10, 2024)
5-151794222-G-T		not specified	Uncertain significance (Feb 21, 2024)
5-151794250-G-T			Uncertain significance (Mar 26, 2024)
5-151795491-A-T		not specified	Uncertain significance (Feb 21, 2024)
5-151795545-C-A		not specified	Uncertain significance (May 23, 2024)
5-151795572-T-A			Uncertain significance (Apr 23, 2024)
5-151797244-A-G		not specified	Uncertain significance (Feb 27, 2024)
5-151797267-C-T			Uncertain significance (May 21, 2024)
5-151797301-A-C		not specified	Uncertain significance (Sep 26, 2024)
5-151797355-C-G		not specified	Uncertain significance (Apr 23, 2024)
5-151797363-G-A		not specified	Uncertain significance (Jul 02, 2024)
5-151797379-C-A		not specified	Uncertain significance (Jul 09, 2021)
5-151797394-C-T		not specified	Uncertain significance (Mar 01, 2025)
5-151799251-C-T		not specified	Uncertain significance (Feb 16, 2023)
5-151799311-C-T			Uncertain significance (May 23, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
G3BP1	protein_coding	protein_coding	ENST00000394123	11	41741

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0331	0.967	125726	0	20	125746	0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.86	182	268	0.680	0.0000145	3054
Missense in Polyphen		19	45.613	0.41655		580
Synonymous	0.0314	89	89.4	0.996	0.00000445	919
Loss of Function	3.48	8	27.8	0.288	0.00000177	282

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000127	0.000119
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000114	0.000114
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000657	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: ATP- and magnesium-dependent helicase (PubMed:9889278). Unwinds preferentially partial DNA and RNA duplexes having a 17 bp annealed portion and either a hanging 3' tail or hanging tails at both 5'- and 3'-ends (PubMed:9889278). Unwinds DNA/DNA, RNA/DNA, and RNA/RNA substrates with comparable efficiency (PubMed:9889278). Acts unidirectionally by moving in the 5' to 3' direction along the bound single-stranded DNA (PubMed:9889278). Phosphorylation-dependent sequence-specific endoribonuclease in vitro (PubMed:11604510). Cleaves exclusively between cytosine and adenine and cleaves MYC mRNA preferentially at the 3'-UTR (PubMed:11604510). May be a regulated effector of stress granule assembly (PubMed:12642610, PubMed:20180778). {ECO:0000269|PubMed:11604510, ECO:0000269|PubMed:12642610, ECO:0000269|PubMed:20180778, ECO:0000269|PubMed:9889278}.

Recessive Scores

• pRec: 0.163

Intolerance Scores

• loftool: 0.714
• rvis_EVS: -0.36
• rvis_percentile_EVS: 28.63

Haploinsufficiency Scores

• pHI: 0.917
• hipred: Y
• hipred_score: 0.785
• ghis: 0.706

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.997

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: G3bp1
• Phenotype: growth/size/body region phenotype; craniofacial phenotype; cellular phenotype; embryo phenotype; respiratory system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); 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); limbs/digits/tail phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: Ras protein signal transduction;DNA duplex unwinding;stress granule assembly;negative regulation of canonical Wnt signaling pathway;nucleic acid phosphodiester bond hydrolysis
• Cellular component: nucleus;cytosol;focal adhesion;cytoplasmic stress granule;perikaryon;ribonucleoprotein complex
• Molecular function: DNA binding;RNA binding;mRNA binding;ATP-dependent DNA helicase activity;ATP-dependent RNA helicase activity;endonuclease activity;protein binding;ATP binding