EVI5

protein-coding

ecotropic viral integration site 5

Gene summary

Enables GTPase activator activity and small GTPase binding activity. Involved in positive regulation of GTPase activity and retrograde transport, endosome to Golgi. Located in cytosol. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001350197.2

Inheritance

—

ClinVar variants

U:110B:5

Top phenotype

EVI5-related disorder

gnomAD constraint

pLI —, LoF o/e 0.54

Max pathogenic AF

—

Genomic locus

chr1:92,508,696-92,792,404

External References & Databases

Ensembl (ENSG00000067208)

Transcript & Mutation Effects

hg38 • Region Span ~283.7 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 EVI5 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 105

not providedTotal: 3

EVI5-related disorderTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001350197.2. 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			1 clinvar	1 clinvar	1 clinvar	3
missense			106 clinvar	3 clinvar		109
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	110	4	1	115

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 76 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001350197.2	RefSeq	NP_001337126.1	19	MANE Select
ENST00000684568.2	Ensembl	ENSP00000506999.1	19	MANE Select
NM_001308248.2	RefSeq	NP_001295177.1	19	Standard
NM_001350198.2	RefSeq	NP_001337127.1	20	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Aurora B signaling

Biological Process

intracellular protein transport
cell cycle
multicellular organism development
cell population proliferation
retrograde transport, endosome to Golgi

Molecular Function

GTPase activator activity
protein binding
Rab GTPase binding

Cellular Component

nucleus
Golgi apparatus
microtubule organizing center
spindle
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000370331
Coding exons: 18
Length: 283709
Individuals with no LoFs: 125515
Homozygous LoFs: 1
Heterozygous LoFs: 232
Defined: 125748
p: 0.000927

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.780	370	415	0.892	0.0000207	5359
Missense (PolyPhen)		65	100.84	0.64459		1282
Synonymous	0.598	134	143	0.936	0.00000748	1446
Loss of Function	2.86	25	45.9	0.545	0.00000229	562

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00062	0.00062	rare
Latino/Admixed American	0.00063	0.00058	rare
Ashkenazi Jewish	0.0092	0.0090	notable
East Asian	0.00038	0.00038	rare
Finnish	0.00067	0.00065	rare
European (Non-Finnish)	0.00062	0.00060	rare
South Asian	0.00066	0.00062	rare
Other	0.00084	0.00081	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Functions as a regulator of cell cycle progression by stabilizing the FBXO5 protein and promoting cyclin-A accumulation during interphase. May play a role in cytokinesis. {ECO:0000269|PubMed:16439210}.;
Disease: DISEASE: Note=A chromosomal aberration involving EVI5 is found is a patient with stage 4S neuroblastoma. Translocation t(1;10)(p22;q21) that forms a EVI5-TRNG10 fusion protein. TRNG10 is a probable structural transcript which is normally not translated. {ECO:0000269|PubMed:9618176}.;

Recessive Scores

pRec: 0.106

Intolerance Scores

LoFtool: 0.975
RVIS EVS: 0.18
RVIS percentile EVS: 66.13

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.764

Gene Damage Prediction

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