EPN3

protein-coding

epsin 3

Gene summary

Predicted to enable clathrin binding activity and phospholipid binding activity. Predicted to be involved in endocytosis. Located in several cellular components, including clathrin-coated vesicle; cytoplasmic side of plasma membrane; and perinuclear region of cytoplasm. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_017957.3

Inheritance

—

ClinVar variants

U:145B:9

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.99

Max pathogenic AF

—

Genomic locus

chr17:50,532,682-50,543,750

External References & Databases

Ensembl (ENSG00000049283)

Transcript & Mutation Effects

hg38 • Region Span ~11.1 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 EPN3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 149

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_017957.3. 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	2 clinvar		3
missense			143 clinvar	6 clinvar		149
nonsense						0
start loss						0
frameshift					1 clinvar	1
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	145	8	1	154

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 31 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_017957.3	RefSeq	NP_060427.2	9	MANE Select
ENST00000268933.8	Ensembl	ENSP00000268933.3	9	MANE Select
ENST00000503246.1	Ensembl	ENSP00000426762.1	1	Standard
ENST00000503690.5	Ensembl	ENSP00000424306.1	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Endocytosis - Homo sapiens (human)
EGFR1

Molecular Function

protein binding
lipid binding
EH domain binding

Cellular Component

nucleus
nucleoplasm
clathrin-coated pit
extrinsic component of plasma membrane
clathrin-coated vesicle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000268933
Coding exons: 9
Length: 11208
Individuals with no LoFs: 124908
Homozygous LoFs: 11
Heterozygous LoFs: 829
Defined: 125748
p: 0.00335

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.584	424	392	1.08	0.0000245	3985
Missense (PolyPhen)		175	152.1	1.1506		1473
Synonymous	-1.57	203	176	1.15	0.0000112	1379
Loss of Function	0.0661	25	25.4	0.986	0.00000134	261

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00056	0.00055	rare
Latino/Admixed American	0.017	0.017	notable
Ashkenazi Jewish	0.0011	0.0011	notable
East Asian	0.0014	0.0014	notable
Finnish	0.00028	0.00028	rare
European (Non-Finnish)	0.0016	0.0016	notable
South Asian	0.00064	0.00062	rare
Other	0.0031	0.0031	notable

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0929

Intolerance Scores

LoFtool: 0.816
RVIS EVS: 1.14
RVIS percentile EVS: 92.37

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): H
Indispensability pred.: N
Indispensability score: 0.137

Gene Damage Prediction

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