ENTREP2

endosomal transmembrane epsin interactor 2

Basic information

Region (hg38): 15:29120252-29570979

Previous symbols: [ "FAM189A1" ]

Links

ENSG00000104059 ∙ NCBI:23359 ∙ OMIM:620052 ∙ HGNC:29075 ∙ Uniprot:O60320 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ENTREP2 gene.

• Lung disease, immunodeficiency, and chromosome breakage syndrome; (2 variants)
• Lung damage, immunodeficiency and chromosome breakage syndrome (2 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ENTREP2 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			40	2	1	43
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding	2		74	97	6	179
Total	2	0	114	100	7

Highest pathogenic variant AF is 0.0000526

Variants in ENTREP2

This is a list of pathogenic ClinVar variants found in the ENTREP2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
15-29123362-C-T		not specified	Uncertain significance (Aug 12, 2021)
15-29123388-C-T		not specified	Uncertain significance (Oct 10, 2023)
15-29123412-C-A		not specified	Uncertain significance (Mar 30, 2024)
15-29123520-A-G		not specified	Uncertain significance (Mar 07, 2024)
15-29123568-G-C		not specified	Uncertain significance (May 27, 2022)
15-29123571-C-T		not specified	Uncertain significance (Jul 12, 2023)
15-29123572-G-A		not specified	Uncertain significance (Feb 06, 2024)
15-29123573-T-A		not specified	Uncertain significance (Mar 29, 2024)
15-29123587-A-G		not specified	Uncertain significance (Apr 15, 2024)
15-29123602-C-A		not specified	Uncertain significance (Oct 27, 2023)
15-29123604-G-A		not specified	Uncertain significance (Oct 05, 2023)
15-29123655-G-A		not specified	Likely benign (Apr 07, 2022)
15-29124688-G-C		not specified	Uncertain significance (May 30, 2023)
15-29124717-C-T		not specified	Uncertain significance (Dec 06, 2021)
15-29124737-G-C		not specified	Uncertain significance (May 20, 2024)
15-29124740-G-A		not specified	Uncertain significance (Mar 01, 2023)
15-29126291-T-G		not specified	Uncertain significance (Dec 18, 2023)
15-29126308-C-T		not specified	Uncertain significance (Aug 30, 2022)
15-29126370-AT-GC		not specified	Benign (-)
15-29126378-G-A		not specified	Uncertain significance (May 11, 2022)
15-29126394-G-T			Likely benign (Jan 01, 2023)
15-29128822-C-T		not specified	Uncertain significance (Apr 09, 2024)
15-29128825-C-T		not specified	Uncertain significance (Aug 13, 2021)
15-29128837-C-T		not specified	Uncertain significance (May 25, 2022)
15-29128856-A-C			Likely benign (Jul 05, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ENTREP2	protein_coding	protein_coding	ENST00000261275	11	450471

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0393	0.955	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.11	214	265	0.808	0.0000157	3417
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 1.46
• rvis_percentile_EVS: 95.18

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00693

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fam189a1

Gene ontology

• Cellular component: integral component of membrane