ENTREP1

protein-coding

endosomal transmembrane epsin interactor 1

Gene summary

Enables ubiquitin ligase activator activity. Involved in CXCL12-activated CXCR4 signaling pathway and negative adaptation of signaling pathway. Located in endosome membrane and plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C9orf61
FAM189A2

MANE transcript

NM_001347995.2

Inheritance

—

ClinVar variants

U:84B:18

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.74

Max pathogenic AF

—

Genomic locus

chr9:69,324,567-69,392,558

External References & Databases

Ensembl (ENSG00000135063)

Transcript & Mutation Effects

hg38 • Region Span ~68.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

schizophreniaNO_KNOWN

Inheritance Pattern: Unknown

Disease ID:MONDO:0005090

Submitter: Labcorp Genetics (formerly Invitae)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ENTREP1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 94

not providedTotal: 16

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001347995.2. 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				6 clinvar	1 clinvar	7
missense			81 clinvar	8 clinvar	2 clinvar	91
nonsense				1 clinvar		1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	84	15	3	102

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 33 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001347995.2	RefSeq	NP_001334924.1	11	MANE Select
ENST00000303068.14	Ensembl	ENSP00000304435.8	11	MANE Select
NM_001127608.3	RefSeq	NP_001121080.1	10	Standard
NM_004816.5	RefSeq	NP_004807.3	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

biological_process

Molecular Function

molecular_function

Cellular Component

cellular_component
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000257515
Coding exons: 10
Length: 67884
Individuals with no LoFs: 125605
Homozygous LoFs: 0
Heterozygous LoFs: 143
Defined: 125748
p: 0.000569

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.620	237	265	0.893	0.0000151	2892
Missense (PolyPhen)		86	96.858	0.8879		1112
Synonymous	1.45	88	107	0.821	0.00000647	950
Loss of Function	1.15	17	22.9	0.741	0.00000139	245

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0022	0.0022	notable
Latino/Admixed American	0.0013	0.0013	notable
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.0015	0.0015	notable
Finnish	0.00032	0.00032	rare
European (Non-Finnish)	0.00013	0.00013	rare
South Asian	0.00029	0.00029	rare
Other	0.00049	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0908

Intolerance Scores

LoFtool: 0.941
RVIS EVS: -0.29
RVIS percentile EVS: 33.34

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.539

Gene Damage Prediction

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