EIF4A1

protein-coding

eukaryotic translation initiation factor 4A1, the group of Small nucleolar RNA protein coding host genes|DEAD-box helicases

Gene summary

Enables double-stranded RNA binding activity and translation initiation factor activity. Involved in cytoplasmic translational initiation and positive regulation of transcription by RNA polymerase II. Located in nuclear stress granule; perinuclear region of cytoplasm; and plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

EIF4A

MANE transcript

NM_001416.4

Inheritance

—

ClinVar variants

U:16B:2

Top phenotype

Autism spectrum disorder

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr17:7,572,824-7,579,006

External References & Databases

Ensembl (ENSG00000161960)

Transcript & Mutation Effects

hg38 • Region Span ~6.2 kb

Loading mutation effect viewer...

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 EIF4A1 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 14

not providedTotal: 2

Autism spectrum disorderTotal: 1

See casesTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001416.4. 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				2 clinvar		2
missense			13 clinvar			13
nonsense			1 clinvar			1
start loss						0
frameshift			2 clinvar			2
splice donor/acceptor (+/-2bp)						0
Total	0	0	16	2	0	18

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 124 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001416.4	RefSeq	NP_001407.1	11	MANE Select
ENST00000293831.13	Ensembl	ENSP00000293831.8	11	MANE Select
NM_001204510.2	RefSeq	NP_001191439.1	11	Standard
ENST00000577269.5	Ensembl	ENSP00000463486.1	11	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
eif4a1a	Danio rerio	Structure: trunk Quality: necrotic abnormal

Gene / Model

Organism

Observed Phenotype

eif4a1a

Danio rerio

Structure: trunk

Quality: necrotic

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

RNA transport - Homo sapiens (human)
Translation Factors
Interferon type I signaling pathways
mtor signaling pathway
regulation of eif-4e and p70s6 kinase

Biological Process

translational initiation
viral process

Molecular Function

RNA cap binding
RNA binding
double-stranded RNA binding
mRNA binding
translation initiation factor activity

Cellular Component

nucleus
cytoplasm
cytosol
membrane
eukaryotic translation initiation factor 4F complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000293831
Coding exons: 11
Length: 6300
Individuals with no LoFs: 117562
Homozygous LoFs: 0
Heterozygous LoFs: 1
Defined: 117563
p: 0.00000425

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	3.93	74	248	0.298	0.0000141	2679
Missense (PolyPhen)		12	88.757	0.1352		1076
Synonymous	-4.09	138	88.9	1.55	0.00000504	775
Loss of Function	4.67	0	25.4	0.00	0.00000156	254

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.0000093	0.0000093	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: ATP-dependent RNA helicase which is a subunit of the eIF4F complex involved in cap recognition and is required for mRNA binding to ribosome. In the current model of translation initiation, eIF4A unwinds RNA secondary structures in the 5'-UTR of mRNAs which is necessary to allow efficient binding of the small ribosomal subunit, and subsequent scanning for the initiator codon. {ECO:0000269|PubMed:19153607, ECO:0000269|PubMed:19204291}.;

Recessive Scores

pRec: 0.426

Intolerance Scores

LoFtool: 0.321
RVIS EVS: -0.36
RVIS percentile EVS: 28.63

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.992

Gene Damage Prediction

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