ENTR1

endosome associated trafficking regulator 1

Basic information

Region (hg38): 9:136401921-136410614

Previous symbols: [ "SDCCAG3" ]

Links

ENSG00000165689 ∙ NCBI:10807 ∙ OMIM:618289 ∙ HGNC:10667 ∙ Uniprot:Q96C92 ∙ 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 ENTR1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ENTR1 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						0
missense			38	1		39
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					3	3
Total	0	0	38	1	3

Variants in ENTR1

This is a list of pathogenic ClinVar variants found in the ENTR1 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-136402825-C-G		not specified	Uncertain significance (Jul 05, 2023)
9-136402830-T-C		not specified	Uncertain significance (Feb 12, 2024)
9-136402847-C-T		not specified	Uncertain significance (Aug 17, 2022)
9-136404113-C-T		not specified	Likely benign (May 25, 2022)
9-136404116-T-C		not specified	Uncertain significance (Jan 10, 2023)
9-136404139-G-A		not specified	Uncertain significance (Jun 13, 2022)
9-136404142-C-G		not specified	Uncertain significance (Oct 12, 2021)
9-136404145-T-G		not specified	Uncertain significance (Mar 24, 2023)
9-136404149-C-T		not specified	Uncertain significance (Jan 23, 2023)
9-136404181-T-C		not specified	Uncertain significance (May 03, 2023)
9-136405150-C-T		not specified	Uncertain significance (Mar 07, 2024)
9-136405164-A-G		not specified	Uncertain significance (Jan 26, 2023)
9-136405931-C-G		not specified	Uncertain significance (Oct 26, 2022)
9-136405967-T-G		not specified	Uncertain significance (Oct 03, 2022)
9-136405972-C-T		not specified	Uncertain significance (Nov 09, 2021)
9-136407167-G-A		not specified	Uncertain significance (Oct 02, 2023)
9-136407171-G-A		not specified	Uncertain significance (Dec 21, 2022)
9-136407206-G-A		not specified	Uncertain significance (Aug 12, 2022)
9-136407249-C-T		not specified	Uncertain significance (May 03, 2023)
9-136407251-C-T		not specified	Uncertain significance (Mar 07, 2024)
9-136407305-T-C		not specified	Uncertain significance (Feb 28, 2023)
9-136407315-T-C		not specified	Uncertain significance (Jan 24, 2024)
9-136407379-C-G		not specified	Uncertain significance (Dec 26, 2023)
9-136407390-C-T		not specified	Uncertain significance (Dec 14, 2022)
9-136407414-A-C		not specified	Uncertain significance (Apr 12, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ENTR1	protein_coding	protein_coding	ENST00000357365	10	8685

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.65e-13	0.0450	124676	0	123	124799	0.000493

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.11	309	259	1.19	0.0000155	2785
Missense in Polyphen		49	41.975	1.1674		580
Synonymous	-3.04	166	123	1.35	0.00000905	883
Loss of Function	0.291	20	21.5	0.932	0.00000110	242

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00111	0.00111
Ashkenazi Jewish	0.0000993	0.0000993
East Asian	0.000893	0.000890
Finnish	0.000141	0.000139
European (Non-Finnish)	0.000451	0.000441
Middle Eastern	0.000893	0.000890
South Asian	0.000730	0.000719
Other	0.000166	0.000165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Endosome-associated protein that plays a role in membrane receptor sorting, cytokinesis and ciliogenesis (PubMed:23108400, PubMed:25278552, PubMed:27767179). Involved in the endosome-to-plasma membrane trafficking and recycling of SNX27-retromer-dependent cargo proteins, such as GLUT1 (PubMed:25278552). Involved in the regulation of cytokinesis; the function may involve PTPN13 and GIT1 (PubMed:23108400). Plays a role in the formation of cilia (PubMed:27767179). Involved in cargo protein localization, such as PKD2, at primary cilia (PubMed:27767179). Involved in the presentation of the tumor necrosis factor (TNF) receptor TNFRSF1A on the cell surface, and hence in the modulation of the TNF-induced apoptosis (By similarity). {ECO:0000250|UniProtKB:A2AIW0, ECO:0000269|PubMed:23108400, ECO:0000269|PubMed:25278552, ECO:0000269|PubMed:27767179}.

Recessive Scores

• pRec: 0.103

Intolerance Scores

• rvis_EVS: 0.47
• rvis_percentile_EVS: 78.8

Haploinsufficiency Scores

• pHI: 0.139
• hipred: N
• hipred_score: 0.170
• ghis: 0.573

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Entr1

Gene ontology

• Biological process: cell cycle;protein transport;cell projection organization;regulation of cytokinesis;positive regulation of cilium assembly;cell division;positive regulation of protein localization to cilium;retrograde transport, endosome to plasma membrane
• Cellular component: endosome;early endosome;centrosome;midbody;retromer complex;ciliary basal body;recycling endosome
• Molecular function: protein binding