ENTREP3

protein-coding

endosomal transmembrane epsin interactor 3

Gene summary

This gene is located near the gene for the lysosomal enzyme glucosylceramidase; a deficiency in this enzyme is associated with Gaucher disease. The encoded protein has been identified as a potential binding partner of a WW domain-containing protein which is involved in apoptosis and tumor suppression. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2010]

Previous symbols:

C1orf2
FAM189B

MANE transcript

NM_006589.3

Inheritance

—

ClinVar variants

U:118

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.47

Max pathogenic AF

—

Genomic locus

chr1:155,247,205-155,255,483

External References & Databases

Ensembl (ENSG00000160767)

Transcript & Mutation Effects

hg38 • Region Span ~8.3 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 ENTREP3 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 108

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_006589.3. 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			2 clinvar			2
missense			111 clinvar			111
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	118	0	0	118

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 58 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_006589.3	RefSeq	NP_006580.2	12	MANE Select
ENST00000361361.7	Ensembl	ENSP00000354958.2	12	MANE Select
NM_001267608.2	RefSeq	NP_001254537.1	11	Standard
NM_198264.2	RefSeq	NP_937995.1	9	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

biological_process

Molecular Function

protein binding
WW domain binding

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000361361
Coding exons: 12
Length: 8279
Individuals with no LoFs: 125466
Homozygous LoFs: 1
Heterozygous LoFs: 281
Defined: 125748
p: 0.00112

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.683	339	376	0.901	0.0000224	4128
Missense (PolyPhen)		162	196.35	0.82505		2230
Synonymous	0.655	148	159	0.934	0.00000907	1528
Loss of Function	2.56	13	27.5	0.472	0.00000165	283

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0011	0.0010	notable
Latino/Admixed American	0.00055	0.00052	rare
Ashkenazi Jewish	0.0077	0.0075	notable
East Asian	0.00011	0.00011	rare
Finnish	0.00077	0.00065	rare
European (Non-Finnish)	0.0013	0.0012	notable
South Asian	0.000068	0.000065	rare
Other	0.0026	0.0024	notable

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.117

Intolerance Scores

LoFtool: 0.863
RVIS EVS: 0.13
RVIS percentile EVS: 63.49

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.231

Gene Damage Prediction

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