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GeneBe

ENTR1

endosome associated trafficking regulator 1

Basic information

Region (hg38): 9:136401921-136410614

Previous symbols: [ "SDCCAG3" ]

Links

ENSG00000165689NCBI:10807OMIM:618289HGNC:10667Uniprot:Q96C92AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ENTR1 gene.

  • Inborn genetic diseases (9 variants)
  • not provided (3 variants)

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
9
clinvar
9
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
3
clinvar
3
Total 0 0 9 0 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)2594931
9-136402830-T-C not specified Uncertain significance (Feb 12, 2024)3089140
9-136402847-C-T not specified Uncertain significance (Aug 17, 2022)3089138
9-136404113-C-T not specified Likely benign (May 25, 2022)3089137
9-136404116-T-C not specified Uncertain significance (Jan 10, 2023)2474638
9-136404139-G-A not specified Uncertain significance (Jun 13, 2022)3089136
9-136404142-C-G not specified Uncertain significance (Oct 12, 2021)3089135
9-136404145-T-G not specified Uncertain significance (Mar 24, 2023)2522625
9-136404149-C-T not specified Uncertain significance (Jan 23, 2023)2465727
9-136404181-T-C not specified Uncertain significance (May 03, 2023)2511467
9-136405150-C-T not specified Uncertain significance (Mar 07, 2024)3089164
9-136405164-A-G not specified Uncertain significance (Jan 26, 2023)2479841
9-136405931-C-G not specified Uncertain significance (Oct 26, 2022)3089163
9-136405967-T-G not specified Uncertain significance (Oct 03, 2022)3089162
9-136405972-C-T not specified Uncertain significance (Nov 09, 2021)3089161
9-136407167-G-A not specified Uncertain significance (Oct 02, 2023)3089160
9-136407171-G-A not specified Uncertain significance (Dec 21, 2022)3089159
9-136407206-G-A not specified Uncertain significance (Aug 12, 2022)3089158
9-136407249-C-T not specified Uncertain significance (May 03, 2023)2555361
9-136407251-C-T not specified Uncertain significance (Mar 07, 2024)3089157
9-136407305-T-C not specified Uncertain significance (Feb 28, 2023)3089156
9-136407315-T-C not specified Uncertain significance (Jan 24, 2024)3089155
9-136407379-C-G not specified Uncertain significance (Dec 26, 2023)3089154
9-136407390-C-T not specified Uncertain significance (Dec 14, 2022)3089153
9-136407414-A-C not specified Uncertain significance (Apr 12, 2022)3089152

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
ENTR1protein_codingprotein_codingENST00000357365 108685
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
3.65e-130.045012467601231247990.000493
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-1.113092591.190.00001552785
Missense in Polyphen4941.9751.1674580
Synonymous-3.041661231.350.00000905883
Loss of Function0.2912021.50.9320.00000110242

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.001110.00111
Ashkenazi Jewish0.00009930.0000993
East Asian0.0008930.000890
Finnish0.0001410.000139
European (Non-Finnish)0.0004510.000441
Middle Eastern0.0008930.000890
South Asian0.0007300.000719
Other0.0001660.000165

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

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