EIF5A2

eukaryotic translation initiation factor 5A2

Basic information

Region (hg38): 3:170888418-170908644

Links

ENSG00000163577NCBI:56648OMIM:605782HGNC:3301Uniprot:Q9GZV4AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the EIF5A2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EIF5A2 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
0
missense
6
clinvar
6
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 6 0 0

Variants in EIF5A2

This is a list of pathogenic ClinVar variants found in the EIF5A2 region.

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

Position Type Phenotype Significance ClinVar
3-170893377-T-C not specified Uncertain significance (Aug 17, 2021)2245996
3-170893408-C-G not specified Uncertain significance (Jun 23, 2021)2233047
3-170894297-C-G not specified Uncertain significance (May 23, 2024)3275079
3-170894311-T-C not specified Uncertain significance (Dec 11, 2023)3088080
3-170907089-T-C not specified Uncertain significance (Sep 14, 2022)2312281
3-170907700-C-T not specified Uncertain significance (Mar 22, 2023)2528379
3-170907797-C-T not specified Uncertain significance (Oct 12, 2022)2406251

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
EIF5A2protein_codingprotein_codingENST00000295822 420279
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.0002110.5131257370111257480.0000437
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.245385.10.6230.000004191000
Missense in Polyphen917.3650.51827234
Synonymous0.2992729.10.9290.00000156285
Loss of Function0.40467.170.8373.73e-790

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00002900.0000290
Ashkenazi Jewish0.000.00
East Asian0.00005450.0000544
Finnish0.000.00
European (Non-Finnish)0.00007060.0000703
Middle Eastern0.00005450.0000544
South Asian0.00003320.0000327
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. Functions as a regulator of 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 (By similarity). {ECO:0000250, ECO:0000269|PubMed:14622290}.;
Pathway
EMT transition in Colorectal Cancer;Post-translational protein modification;Metabolism of proteins;Gamma carboxylation, hypusine formation and arylsulfatase activation;Hypusine synthesis from eIF5A-lysine (Consensus)

Recessive Scores

pRec
0.136

Intolerance Scores

loftool
0.540
rvis_EVS
0.08
rvis_percentile_EVS
59.43

Haploinsufficiency Scores

pHI
0.492
hipred
N
hipred_score
0.459
ghis
0.601

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.781

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Eif5a2
Phenotype
normal phenotype;

Gene ontology

Biological process
translational frameshifting;spermatogenesis;positive regulation of cell population proliferation;polyamine homeostasis;protein transport;positive regulation of translational elongation;positive regulation of translational termination;mRNA transport
Cellular component
nuclear pore;endoplasmic reticulum membrane;cytosol;intracellular membrane-bounded organelle
Molecular function
translation elongation factor activity;protein binding;ribosome binding