EIF4E3

protein-coding

eukaryotic translation initiation factor 4E family member 3

Gene summary

EIF4E3 belongs to the EIF4E family of translational initiation factors that interact with the 5-prime cap structure of mRNA and recruit mRNA to the ribosome (Joshi et al., 2004 [PubMed 15153109]).[supplied by OMIM, Mar 2008]

MANE transcript

NM_001134651.2

Inheritance

—

ClinVar variants

U:40

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.39

Max pathogenic AF

—

Genomic locus

chr3:71,675,414-71,754,773

External References & Databases

Ensembl (ENSG00000163412)

Transcript & Mutation Effects

hg38 • Region Span ~79.4 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 EIF4E3 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 36

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001134651.2. 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			1 clinvar			1
missense			37 clinvar			37
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	40	0	0	40

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 38 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001134651.2	RefSeq	NP_001128123.1	7	MANE Select
ENST00000425534.8	Ensembl	ENSP00000393324.2	7	MANE Select
NM_001134649.3	RefSeq	NP_001128121.1	5	Standard
NM_001134650.1	RefSeq	NP_001128122.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Cytokine Signaling in Immune system
Immune System
ISG15 antiviral mechanism
Antiviral mechanism by IFN-stimulated genes
Interferon Signaling

Biological Process

translational initiation
regulation of translation

Molecular Function

RNA 7-methylguanosine cap binding
translation initiation factor activity

Cellular Component

cytosol
mRNA cap binding complex
eukaryotic translation initiation factor 4F complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000425534
Coding exons: 7
Length: 79358
Individuals with no LoFs: 125719
Homozygous LoFs: 0
Heterozygous LoFs: 26
Defined: 125745
p: 0.000103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.510	78	91.8	0.850	0.00000496	1420
Missense (PolyPhen)		36	47.101	0.76431		604
Synonymous	0.0321	31	31.2	0.993	0.00000169	450
Loss of Function	2.05	5	13.0	0.386	8.14e-7	153

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0.0016	0.0015	notable
East Asian	0.000055	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000078	0.000070	rare
South Asian	0.000033	0.000033	rare
Other	0.00019	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Recognizes and binds the 7-methylguanosine-containing mRNA cap during an early step in the initiation of protein synthesis. May act as an inhibitor of EIF4E1 activity (By similarity). {ECO:0000250}.;

Recessive Scores

pRec: 0.113

Intolerance Scores

LoFtool: 0.784
RVIS EVS: -0.1
RVIS percentile EVS: 46.2

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.539

Gene Damage Prediction

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