EIF5A

eukaryotic translation initiation factor 5A

Basic information

Region (hg38): 17:7306999-7312463

Links

ENSG00000132507NCBI:1984OMIM:600187HGNC:3300Uniprot:P63241AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • Faundes-Banka syndrome (Strong), mode of inheritance: AD
  • Faundes-Banka syndrome (Moderate), mode of inheritance: AD
  • Faundes-Banka syndrome (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Faundes-Banka syndromeADCardiovascularIndividuals may have congenital cardiovascular anomalies, and awareness may allow early identification and managementCardiovascular; Craniofacial; Neurologic33547280

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the EIF5A gene.

  • not_provided (16 variants)
  • Faundes-Banka_syndrome (9 variants)
  • not_specified (9 variants)
  • Neurodevelopmental_disorder (1 variants)
  • EIF5A-related_disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EIF5A gene is commonly pathogenic or not. These statistics are base on transcript: NM_000001970.5. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
2
clinvar
2
missense
3
clinvar
4
clinvar
14
clinvar
21
nonsense
1
clinvar
1
start loss
0
frameshift
2
clinvar
2
clinvar
1
clinvar
5
splice donor/acceptor (+/-2bp)
2
clinvar
2
Total 5 9 15 2 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
EIF5Aprotein_codingprotein_codingENST00000336452 55457
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.7370.261125746021257480.00000795
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.41351040.3360.000006011199
Missense in Polyphen020.380266
Synonymous-1.835641.11.360.00000276353
Loss of Function2.4318.740.1144.70e-7112

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00005790.0000579
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.000.00
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: mRNA-binding protein involved in translation elongation. Has an important function at the level of mRNA turnover, probably acting downstream of decapping. Involved in actin dynamics and cell cycle progression, mRNA decay and probably in a pathway involved in stress response and maintenance of cell wall integrity. With syntenin SDCBP, functions as a regulator of p53/TP53 and p53/TP53-dependent apoptosis. Regulates also TNF- alpha-mediated apoptosis. Mediates effects of polyamines on neuronal process extension and survival. May play an important role in brain development and function, and in skeletal muscle stem cell differentiation. Also described as a cellular cofactor of human T-cell leukemia virus type I (HTLV-1) Rex protein and of human immunodeficiency virus type 1 (HIV-1) Rev protein, essential for mRNA export of retroviral transcripts. {ECO:0000269|PubMed:15371445, ECO:0000269|PubMed:15452064, ECO:0000269|PubMed:16987817, ECO:0000269|PubMed:17187778, ECO:0000269|PubMed:17360499}.;
Pathway
Translation Factors;eIF5A regulation in response to inhibition of the nuclear export system;Post-translational protein modification;Metabolism of proteins;Gamma carboxylation, hypusine formation and arylsulfatase activation;Hypusine synthesis from eIF5A-lysine (Consensus)

Recessive Scores

pRec
0.298

Intolerance Scores

loftool
0.286
rvis_EVS
-0.05
rvis_percentile_EVS
49.39

Haploinsufficiency Scores

pHI
hipred
Y
hipred_score
0.598
ghis
0.632

Essentials

essential_gene_CRISPR
E
essential_gene_CRISPR2
N
essential_gene_gene_trap
E
gene_indispensability_pred
E
gene_indispensability_score
0.996

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumLowLow
Primary ImmunodeficiencyMediumLowMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Eif5a
Phenotype

Gene ontology

Biological process
mRNA export from nucleus;translational frameshifting;protein export from nucleus;nucleocytoplasmic transport;apoptotic process;positive regulation of cytosolic calcium ion concentration;aging;positive regulation of cell population proliferation;positive regulation of cardiac muscle cell apoptotic process;negative regulation of apoptotic process;positive regulation of translational elongation;positive regulation of translational termination;positive regulation of muscle cell differentiation;cellular response to thyroid hormone stimulus;positive regulation of reactive oxygen species metabolic process
Cellular component
nucleus;annulate lamellae;nuclear pore;cytoplasm;endoplasmic reticulum membrane;cytosol;membrane;dendrite;neuronal cell body;synapse
Molecular function
RNA binding;translation elongation factor activity;protein binding;U6 snRNA binding;ribosome binding;protein N-terminus binding