ENTR1
Basic information
Region (hg38): 9:136401921-136410614
Previous symbols: [ "SDCCAG3" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
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 | 39 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region ? | 0 | |||||
non coding ? | 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) | ||
9-136402825-C-T | not specified | Uncertain significance (May 26, 2024) | ||
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) | ||
9-136407236-G-C | not specified | Uncertain significance (Jun 04, 2024) | ||
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) | ||
9-136407308-G-A | not specified | Uncertain significance (Apr 08, 2024) | ||
9-136407315-T-C | not specified | Uncertain significance (Jan 24, 2024) |
GnomAD
Source:
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:
- 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
- loftool
- 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_CRISPR
- essential_gene_CRISPR2
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- gene_indispensability_score
Mouse Genome Informatics
- Gene name
- Entr1
- Phenotype
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