ENTREP2

protein-coding

endosomal transmembrane epsin interactor 2

Gene summary

Predicted to be located in membrane. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

FAM189A1

MANE transcript

NM_015307.2

Inheritance

—

ClinVar variants

U:98B:9

Top phenotype

NSMCE3-related disorder

gnomAD constraint

pLI —, LoF o/e 0.33

Max pathogenic AF

—

Genomic locus

chr15:29,120,252-29,570,979

External References & Databases

Ensembl (ENSG00000104059)

Transcript & Mutation Effects

hg38 • Region Span ~450.7 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 ENTREP2 variants in ClinVar

6 Conditions Cataloged

not providedTotal: 192

not specifiedTotal: 117

NSMCE3-related disorderTotal: 6

Lung disease, immunodeficiency, and chromosome breakage syndrome;Total: 6

Lung damage, immunodeficiency and chromosome breakage syndromeTotal: 2

Congenital portosystemic shuntTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_015307.2. 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
missense			97 clinvar	8 clinvar		105
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	98	9	0	107

Highest pathogenic variant AF is 0.00009850593

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 26 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_015307.2	RefSeq	NP_056122.1	11	MANE Select
ENST00000261275.5	Ensembl	ENSP00000261275.4	11	MANE Select
NM_001387214.1	RefSeq	NP_001374143.1	10	Standard
NM_001387215.1	RefSeq	NP_001374144.1	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000261275
Coding exons: 11
Length: 450471
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.11	214	265	0.808	0.0000157	3417
Missense (PolyPhen)		46	65.8	0.69908		866
Synonymous	0.115	117	119	0.987	0.00000827	1166
Loss of Function	2.40	5	15.1	0.332	6.41e-7	213

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	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

RVIS EVS: 1.46
RVIS percentile EVS: 95.18

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.00693

Gene Damage Prediction

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