EVI5L

protein-coding

ecotropic viral integration site 5 like

Gene summary

Enables GTPase activator activity and small GTPase binding activity. Involved in negative regulation of cilium assembly and positive regulation of GTPase activity. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001159944.3

Inheritance

—

ClinVar variants

U:68B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.09

Max pathogenic AF

—

Genomic locus

chr19:7,830,218-7,864,976

External References & Databases

Ensembl (ENSG00000142459)

Transcript & Mutation Effects

hg38 • Region Span ~34.8 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 EVI5L variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 62

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001159944.3. 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
missense			64 clinvar	1 clinvar		65
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	68	1	0	69

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 38 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001159944.3	RefSeq	NP_001153416.1	19	MANE Select
ENST00000538904.7	Ensembl	ENSP00000445905.1	19	MANE Select
NM_145245.5	RefSeq	NP_660288.1	18	Standard
ENST00000270530.8	Ensembl	ENSP00000270530.3	18	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

intracellular protein transport
positive regulation of GTPase activity
activation of GTPase activity
negative regulation of cilium assembly

Molecular Function

GTPase activator activity
protein binding
Rab GTPase binding

Cellular Component

cell

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000538904
Coding exons: 19
Length: 34744
Individuals with no LoFs: 125735
Homozygous LoFs: 0
Heterozygous LoFs: 2
Defined: 125737
p: 0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	4.23	217	477	0.455	0.0000307	5156
Missense (PolyPhen)		74	182.66	0.40513		1994
Synonymous	2.53	173	221	0.783	0.0000153	1563
Loss of Function	5.49	4	42.7	0.0937	0.00000195	497

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.0000088	0.0000088	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Functions as a GTPase-activating protein (GAP) with a broad specificity. {ECO:0000269|PubMed:16923123}.;

Recessive Scores

pRec: 0.108

Intolerance Scores

LoFtool: 0.231
RVIS EVS: -0.82
RVIS percentile EVS: 11.68

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.978

Gene Damage Prediction

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