ENTREP1

endosomal transmembrane epsin interactor 1

Basic information

Region (hg38): 9:69324567-69392558

Previous symbols: [ "C9orf61", "FAM189A2" ]

Links

ENSG00000135063 ∙ NCBI:9413 ∙ OMIM:607710 ∙ HGNC:24820 ∙ Uniprot:Q15884 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• schizophrenia (No Known Disease Relationship), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ENTREP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ENTREP1 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				6	1	7
missense			28	4	2	34
nonsense				1		1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				7	6	13
non coding				4	16	20
Total	0	0	28	15	19

Variants in ENTREP1

This is a list of pathogenic ClinVar variants found in the ENTREP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-69325606-A-C			Likely benign (Dec 01, 2022)
9-69336219-C-T			Benign (Nov 05, 2018)
9-69336241-C-T			Likely benign (Apr 10, 2018)
9-69371360-G-C			Benign (Nov 12, 2018)
9-69371399-T-C			Benign (Nov 11, 2018)
9-69371400-G-A			Benign (Jun 24, 2018)
9-69371598-A-G		not specified	Uncertain significance (Sep 10, 2024)
9-69371604-G-A		not specified	Uncertain significance (Mar 29, 2022)
9-69371689-A-G			Likely benign (Aug 21, 2018)
9-69371889-A-C			Benign (Nov 11, 2018)
9-69375729-C-T		not specified	Benign (May 09, 2017)
9-69375827-C-T		not specified	Uncertain significance (Nov 06, 2024)
9-69375851-A-G		not specified	Uncertain significance (Nov 25, 2024)
9-69375871-C-G		not specified	Likely benign (Feb 07, 2018)
9-69375906-G-A			Likely benign (Aug 23, 2018)
9-69376112-C-T			Benign (Jun 18, 2021)
9-69377283-C-T			Likely benign (Jul 01, 2018)
9-69377371-A-T		not specified	Uncertain significance (Dec 11, 2023)
9-69377413-C-T		not specified	Uncertain significance (Aug 14, 2024)
9-69377415-G-A		not specified	Uncertain significance (Dec 20, 2023)
9-69377419-G-T		not specified	Uncertain significance (Nov 09, 2024)
9-69377440-G-A		not specified	Uncertain significance (Nov 09, 2022)
9-69377472-T-C		not specified	Uncertain significance (Sep 11, 2024)
9-69377487-T-C		not specified	Benign (Jan 08, 2018)
9-69377647-C-T		not specified	Conflicting classifications of pathogenicity (Oct 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ENTREP1	protein_coding	protein_coding	ENST00000257515	10	67884

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.01e-9	0.511	125605	0	143	125748	0.000569

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.620	237	265	0.893	0.0000151	2892
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00355	0.00350
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.00147	0.00147
Finnish	0.000324	0.000323
European (Non-Finnish)	0.000133	0.000132
Middle Eastern	0.00147	0.00147
South Asian	0.000294	0.000294
Other	0.000489	0.000489

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0908

Intolerance Scores

• loftool: 0.941
• rvis_EVS: -0.29
• rvis_percentile_EVS: 33.34

Haploinsufficiency Scores

• pHI: 0.0931
• hipred: N
• hipred_score: 0.361
• ghis: 0.529

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fam189a2

Gene ontology

• Biological process: biological_process
• Cellular component: cellular_component;integral component of membrane
• Molecular function: molecular_function