EIF4A1

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

Basic information

Region (hg38): 17:7572824-7579006

Previous symbols: [ "EIF4A" ]

Links

ENSG00000161960 ∙ NCBI:1973 ∙ OMIM:602641 ∙ HGNC:3282 ∙ Uniprot:P60842 ∙ 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 EIF4A1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EIF4A1 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					1	1
missense			7	1		8
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1			1
non coding						0
Total	0	0	8	1	1

Variants in EIF4A1

This is a list of pathogenic ClinVar variants found in the EIF4A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-7572853-C-G		not specified	Uncertain significance (Jun 17, 2024)
17-7572861-C-T		not specified	Uncertain significance (Aug 12, 2022)
17-7574271-A-G		not specified	Uncertain significance (Jan 04, 2024)
17-7574290-G-T		not specified	Uncertain significance (Oct 06, 2024)
17-7575180-G-A			Benign (Dec 17, 2021)
17-7575197-A-G		not specified	Uncertain significance (Nov 14, 2024)
17-7575226-G-A		not specified	Uncertain significance (Dec 14, 2023)
17-7577458-C-T		not specified	Uncertain significance (Feb 26, 2024)
17-7577561-A-G		See cases	Uncertain significance (Oct 10, 2018)
17-7577851-C-T		Autism spectrum disorder	Uncertain significance (Aug 16, 2021)
17-7578345-C-T		not specified	Likely benign (Jul 14, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EIF4A1	protein_coding	protein_coding	ENST00000293831	11	6300

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000134	117562	0	1	117563	0.00000425

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.93	74	248	0.298	0.0000141	2679
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000927	0.00000927
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

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}.
• Pathway: RNA transport - Homo sapiens (human);Translation Factors;Interferon type I signaling pathways;mtor signaling pathway;regulation of eif-4e and p70s6 kinase;skeletal muscle hypertrophy is regulated via akt-mtor pathway;internal ribosome entry pathway;Translation initiation complex formation;Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S;Cytokine Signaling in Immune system;Eukaryotic Translation Initiation;Translation;Metabolism of proteins;Metabolism of RNA;Immune System;insulin Mam;eukaryotic protein translation;Ribosomal scanning and start codon recognition;L13a-mediated translational silencing of Ceruloplasmin expression;GTP hydrolysis and joining of the 60S ribosomal subunit;Cap-dependent Translation Initiation;Deadenylation of mRNA;Deadenylation-dependent mRNA decay;mTOR signaling pathway;Validated targets of C-MYC transcriptional activation;ISG15 antiviral mechanism;Antiviral mechanism by IFN-stimulated genes;Interferon Signaling;insulin (Consensus)

Recessive Scores

• pRec: 0.426

Intolerance Scores

• loftool: 0.321
• rvis_EVS: -0.36
• rvis_percentile_EVS: 28.63

Haploinsufficiency Scores

• pHI: 0.994
• hipred: Y
• hipred_score: 0.831
• ghis: 0.654

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.992

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Eif4a1

Zebrafish Information Network

• Gene name: eif4a1a
• Affected structure: trunk
• Phenotype tag: abnormal
• Phenotype quality: necrotic

Gene ontology

• Biological process: translational initiation;viral process
• Cellular component: nucleus;cytoplasm;cytosol;membrane;eukaryotic translation initiation factor 4F complex;extracellular exosome
• Molecular function: RNA cap binding;RNA binding;double-stranded RNA binding;mRNA binding;translation initiation factor activity;ATP-dependent RNA helicase activity;helicase activity;protein binding;ATP binding;translation factor activity, RNA binding