ENTR1
protein-codingendosome associated trafficking regulator 1
Gene summary
Involved in several processes, including endocytic recycling; positive regulation of cilium assembly; and positive regulation of protein localization to cilium. Located in several cellular components, including endosome; microtubule organizing center; and retromer complex. [provided by Alliance of Genome Resources, Jul 2025]
- SDCCAG3
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~8.7 kbGenCC 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 ENTR1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001039707.2. 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 | 0 | |||||
| missense | 112 | 4 | 116 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 5 | 5 | ||||
| Total | 0 | 0 | 118 | 4 | 0 | 122 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001034796.1 | 10 | MANE Select | |
| Ensembl | ENSP00000349929.3 | 10 | MANE Select | |
| RefSeq | NP_001034797.1 | 8 | Standard | |
| RefSeq | NP_006634.3 | 9 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- cell cycle
- protein transport
- cell projection organization
- regulation of cytokinesis
- positive regulation of cilium assembly
Molecular Function
- protein binding
Cellular Component
- endosome
- early endosome
- centrosome
- midbody
- retromer complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000357365
- Coding exons
- 10
- Length
- 8685
- Individuals with no LoFs
- 124676
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 123
- Defined
- 124799
- p
- 0.000493
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -1.11 | 309 | 259 | 1.19 | 0.0000155 | 2785 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00039 | 0.00039 | rare |
| Latino/Admixed American | 0.00072 | 0.00070 | rare |
| Ashkenazi Jewish | 0.000099 | 0.000099 | rare |
| East Asian | 0.00089 | 0.00089 | rare |
| Finnish | 0.00014 | 0.00014 | rare |
| European (Non-Finnish) | 0.00045 | 0.00044 | rare |
| South Asian | 0.00073 | 0.00072 | rare |
| Other | 0.00017 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- 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
Essentials
- Essential (gene trap)
- N