EIF5A2

protein-coding

eukaryotic translation initiation factor 5A2

Gene summary

Predicted to enable translation elongation factor activity. Predicted to be involved in translational elongation. Predicted to be located in cytosol. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_020390.6

Inheritance

—

ClinVar variants

U:10

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.84

Max pathogenic AF

—

Genomic locus

chr3:170,888,418-170,908,644

External References & Databases

Ensembl (ENSG00000163577)

Transcript & Mutation Effects

hg38 • Region Span ~20.2 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 EIF5A2 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 10

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_020390.6. 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						0
missense			10 clinvar			10
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	10	0	0	10

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 9 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_020390.6	RefSeq	NP_065123.1	4	MANE Select
ENST00000295822.7	Ensembl	ENSP00000295822.2	4	MANE Select
ENST00000474096.5	Ensembl	ENSP00000418370.1	3	Standard
ENST00000474417.1	Ensembl	ENSP00000417133.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

EMT transition in Colorectal Cancer
Post-translational protein modification
Metabolism of proteins
Gamma carboxylation, hypusine formation and arylsulfatase activation
Hypusine synthesis from eIF5A-lysine

Biological Process

translational frameshifting
spermatogenesis
positive regulation of cell population proliferation
polyamine homeostasis
protein transport

Molecular Function

translation elongation factor activity
protein binding
ribosome binding

Cellular Component

nuclear pore
endoplasmic reticulum membrane
cytosol
intracellular membrane-bounded organelle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000295822
Coding exons: 4
Length: 20279
Individuals with no LoFs: 125737
Homozygous LoFs: 0
Heterozygous LoFs: 11
Defined: 125748
p: 0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.24	53	85.1	0.623	0.00000419	1000
Missense (PolyPhen)		9	17.365	0.51827		234
Synonymous	0.299	27	29.1	0.929	0.00000156	285
Loss of Function	0.404	6	7.17	0.837	3.73e-7	90

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000055	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000071	0.000070	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.136

Intolerance Scores

LoFtool: 0.540
RVIS EVS: 0.08
RVIS percentile EVS: 59.43

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.781

Gene Damage Prediction

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