EIF4G3

eukaryotic translation initiation factor 4 gamma 3, the group of MIF4G domain containing proteins|MicroRNA protein coding host genes

Basic information

Region (hg38): 1:20806292-21177285

Links

ENSG00000075151 ∙ NCBI:8672 ∙ OMIM:603929 ∙ HGNC:3298 ∙ Uniprot:O43432 ∙ 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 EIF4G3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EIF4G3 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				2		2
missense			95	4	1	100
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	95	7	1

Variants in EIF4G3

This is a list of pathogenic ClinVar variants found in the EIF4G3 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-20807326-T-C		not specified	Uncertain significance (Oct 05, 2023)
1-20807343-T-C			Likely benign (Apr 01, 2023)
1-20807390-C-T		not specified	Uncertain significance (Dec 06, 2022)
1-20807491-C-T		not specified	Uncertain significance (Jan 26, 2022)
1-20810810-A-C		not specified	Uncertain significance (Dec 06, 2021)
1-20810855-C-T		not specified	Uncertain significance (Nov 12, 2021)
1-20810884-G-C		not specified	Uncertain significance (Nov 29, 2023)
1-20813209-G-A		not specified	Uncertain significance (Mar 20, 2024)
1-20813227-C-T		not specified	Uncertain significance (Nov 14, 2024)
1-20817449-G-A			Likely benign (Jun 01, 2024)
1-20817457-T-C		not specified	Uncertain significance (Jun 21, 2023)
1-20817484-T-C		not specified	Uncertain significance (Nov 15, 2021)
1-20817510-G-A		not specified	Uncertain significance (Feb 28, 2024)
1-20817510-G-C		not specified	Uncertain significance (Sep 04, 2024)
1-20817517-C-G		not specified	Uncertain significance (Jul 16, 2021)
1-20817519-G-C		not specified	Uncertain significance (Dec 02, 2024)
1-20817520-A-C		not specified	Uncertain significance (Oct 06, 2021)
1-20817524-T-C		not specified	Uncertain significance (Apr 18, 2023)
1-20827652-G-T		not specified	Uncertain significance (Feb 06, 2023)
1-20829180-T-C		not specified	Uncertain significance (Nov 27, 2023)
1-20829186-A-G			Benign (Sep 29, 2017)
1-20840941-T-G		not specified	Uncertain significance (Aug 21, 2023)
1-20849431-T-G		not specified	Uncertain significance (Dec 09, 2023)
1-20849462-T-C		not specified	Uncertain significance (Jul 14, 2021)
1-20849475-C-A		not specified	Uncertain significance (Jul 20, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EIF4G3	protein_coding	protein_coding	ENST00000602326	31	370415

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	7.90e-11	125730	0	16	125746	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.97	605	848	0.713	0.0000438	10409
Missense in Polyphen		211	388.8	0.54269		4759
Synonymous	0.0494	302	303	0.996	0.0000159	3089
Loss of Function	7.95	4	81.4	0.0491	0.00000446	957

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000801	0.000800
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000267	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable component of the protein complex eIF4F, which is involved in the recognition of the mRNA cap, ATP-dependent unwinding of 5'-terminal secondary structure and recruitment of mRNA to the ribosome. Thought to be a functional homolog of EIF4G1. {ECO:0000269|PubMed:9418880}.
• Pathway: Viral myocarditis - Homo sapiens (human);RNA transport - Homo sapiens (human);Translation Factors;internal ribosome entry pathway;Cytokine Signaling in Immune system;Immune System;insulin Mam;eukaryotic protein translation;ISG15 antiviral mechanism;Antiviral mechanism by IFN-stimulated genes;Interferon Signaling;insulin (Consensus)

Intolerance Scores

• loftool: 0.282
• rvis_EVS: 0.3
• rvis_percentile_EVS: 71.7

Haploinsufficiency Scores

• pHI: 0.665
• hipred: Y
• hipred_score: 0.783
• ghis: 0.484

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.794

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Eif4g3
• Phenotype: cellular phenotype; reproductive system phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: translational initiation;regulation of translational initiation;negative regulation of autophagy
• Cellular component: cytosol;eukaryotic translation initiation factor 4F complex
• Molecular function: RNA cap binding;RNA binding;mRNA binding;translation initiation factor activity;translation factor activity, RNA binding