EVI2A

protein-coding

ecotropic viral integration site 2A

Gene summary

Predicted to enable transmembrane signaling receptor activity. Located in plasma membrane. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

EVI2

MANE transcript

NM_014210.4

Inheritance

—

ClinVar variants

U:41B:9

Top phenotype

EVI2A-related disorder

gnomAD constraint

pLI —, LoF o/e 0.64

Max pathogenic AF

—

Genomic locus

chr17:31,316,410-31,321,749

External References & Databases

Ensembl (ENSG00000126860)

Transcript & Mutation Effects

hg38 • Region Span ~5.3 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 EVI2A variants in ClinVar

8 Conditions Cataloged

not specifiedTotal: 44

not providedTotal: 5

EVI2A-related disorderTotal: 3

Cardiovascular phenotypeTotal: 1

NF1-related disorderTotal: 1

Hereditary cancer-predisposing syndromeTotal: 1

Neurofibromatosis, type 1Total: 1

See casesTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_014210.4. 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			40 clinvar	6 clinvar	1 clinvar	47
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	41	7	2	50

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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_014210.4	RefSeq	NP_055025.2	1	MANE Select
ENST00000462804.3	Ensembl	ENSP00000420557.3	1	MANE Select
NM_001003927.3	RefSeq	NP_001003927.1	2	Standard
ENST00000247270.3	Ensembl	ENSP00000247270.3	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

transmembrane signaling receptor activity

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000247270
Coding exons: 2
Length: 4325
Individuals with no LoFs: 125700
Homozygous LoFs: 0
Heterozygous LoFs: 19
Defined: 125719
p: 0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.0942	140	137	1.02	0.00000658	1698
Missense (PolyPhen)		34	30.781	1.1046		382
Synonymous	-0.903	57	49.0	1.16	0.00000258	512
Loss of Function	0.923	5	7.78	0.643	4.01e-7	93

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00037	0.00037	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00011	0.000088	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May complex with itself or/and other proteins within the membrane, to function as part of a cell-surface receptor.;

Recessive Scores

pRec: 0.0802

Intolerance Scores

LoFtool: 0.362
RVIS EVS: 0.28
RVIS percentile EVS: 71.27

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.123

Gene Damage Prediction

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