ENTR1

gene
On this page

Also known as NY-CO-3

Summary

ENTR1 (endosome associated trafficking regulator 1, HGNC:10667) is a protein-coding gene on chromosome 9q34.3, encoding Endosome-associated-trafficking regulator 1 (Q96C92). Endosome-associated protein that plays a role in membrane receptor sorting, cytokinesis and ciliogenesis.

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.

Source: NCBI Gene 10807 — RefSeq curated summary.

At a glance

  • GWAS associations: 8
  • Clinical variants (ClinVar): 147 total
  • MANE Select transcript: NM_001039707

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:10667
Approved symbolENTR1
Nameendosome associated trafficking regulator 1
Location9q34.3
Locus typegene with protein product
StatusApproved
AliasesNY-CO-3
Ensembl geneENSG00000165689
Ensembl biotypeprotein_coding
OMIM618289
Entrez10807

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 8 protein_coding, 5 protein_coding_CDS_not_defined

ENST00000298537, ENST00000357365, ENST00000371723, ENST00000371725, ENST00000417512, ENST00000446833, ENST00000461693, ENST00000466579, ENST00000468963, ENST00000481114, ENST00000486441, ENST00000918208, ENST00000918209

RefSeq mRNA: 3 — MANE Select: NM_001039707 NM_001039707, NM_001039708, NM_006643

CCDS: CCDS43903, CCDS43904, CCDS6999

Canonical transcript exons

ENST00000357365 — 10 exons

ExonStartEnd
ENSE00001433151136408999136409067
ENSE00001703364136410090136410239
ENSE00001791874136405091136405202
ENSE00001874161136410328136410614
ENSE00002167357136407826136407938
ENSE00003482816136404631136404693
ENSE00003595575136404055136404194
ENSE00003650270136405905136405978
ENSE00003717602136401922136402887
ENSE00003786326136407145136407561

Expression profiles

Bgee: expression breadth ubiquitous, 278 present calls, max score 96.08.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 27.7969 / max 238.3430, expressed in 1815 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
10315515.43881795
10315612.26921782
1031540.089035

Top tissues by expression

290 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
left testisUBERON:000453396.08gold quality
right testisUBERON:000453496.00gold quality
right lobe of liverUBERON:000111495.99gold quality
right hemisphere of cerebellumUBERON:001489095.28gold quality
right ovaryUBERON:000211895.16gold quality
right lobe of thyroid glandUBERON:000111995.08gold quality
body of pancreasUBERON:000115095.03gold quality
granulocyteCL:000009495.01gold quality
cerebellar hemisphereUBERON:000224594.88gold quality
body of uterusUBERON:000985394.78gold quality
spleenUBERON:000210694.75gold quality
cerebellar cortexUBERON:000212994.74gold quality
endocervixUBERON:000045894.72gold quality
peripheral nervous systemUBERON:000001094.68gold quality
nerveUBERON:000102194.68gold quality
tibial nerveUBERON:000132394.68gold quality
skin of abdomenUBERON:000141694.61gold quality
left ovaryUBERON:000211994.60gold quality
lower esophagus mucosaUBERON:003583494.54gold quality
ectocervixUBERON:001224994.53gold quality
metanephros cortexUBERON:001053394.49gold quality
skin of legUBERON:000151194.43gold quality
muscle layer of sigmoid colonUBERON:003580594.19gold quality
right uterine tubeUBERON:000130294.16gold quality
left uterine tubeUBERON:000130394.15gold quality
small intestine Peyer’s patchUBERON:000345494.12gold quality
lower esophagusUBERON:001347394.08gold quality
lower esophagus muscularis layerUBERON:003583394.08gold quality
left lobe of thyroid glandUBERON:000112094.07gold quality
esophagogastric junction muscularis propriaUBERON:003584193.84gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3no0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

23 targeting ENTR1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-314899.9775.066478
HSA-LET-7C-3P99.9573.422862
HSA-MIR-311999.9271.342390
HSA-MIR-808099.8267.521342
HSA-MIR-4760-5P99.8069.881619
HSA-MIR-442299.7272.072908
HSA-MIR-561-3P99.6470.903647
HSA-MIR-217-5P99.4969.931419
HSA-MIR-766-5P99.4767.912225
HSA-MIR-122B-5P99.4670.811457
HSA-MIR-5582-5P99.2771.421879
HSA-MIR-6739-3P99.2268.841843
HSA-MIR-319999.1765.19696
HSA-MIR-805299.1765.01719
HSA-MIR-6807-3P99.1569.231275
HSA-MIR-140-3P99.0467.691324
HSA-MIR-6829-5P98.8665.121480
HSA-MIR-6776-5P98.5467.431304
HSA-MIR-892B98.0067.11821
HSA-MIR-367097.8864.39763
HSA-MIR-514A-5P96.9465.49801
HSA-MIR-6762-5P96.5564.62972
HSA-MIR-6845-5P96.5564.65969

Literature-anchored findings (GeneRIF, showing 4)

  • SDCCAG3 is important for protein trafficking and presentation of TNFR1 on the cell surface. (PMID:16332174)
  • The novel endosomal protein SDCCAG3 forms a complex with PTPN13 & interacts with GIT1. Interaction of SDCCAG3 with PTPN13 is mediated by the PTPN13 FERM domain & the SDCCAG3 N-terminus. SDCCAG3 expression levels are elevated in colon cancers. (PMID:23108400)
  • SDCCAG3 has a role in ciliogenesis and in localization of cargo to primary cilia (PMID:27767179)
  • Endosome associated trafficking regulator 1 promotes tumor growth and invasion of glioblastoma multiforme via inhibiting TNF signaling pathway. (PMID:38191954)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_rerioentr1ENSDARG00000095515
mus_musculusEntr1ENSMUSG00000026927
rattus_norvegicusEntr1l3ENSRNOG00000018876
rattus_norvegicusENSRNOG00000083656
rattus_norvegicusENSRNOG00000085394

Protein

Protein identifiers

Endosome-associated-trafficking regulator 1Q96C92 (reviewed: Q96C92)

Alternative names: Antigen NY-CO-3, Serologically defined colon cancer antigen 3

All UniProt accessions (4): Q96C92, A0A0A0MRP9, B5MDD7, H7C331

UniProt curated annotations — full annotation on UniProt →

Function. Endosome-associated protein that plays a role in membrane receptor sorting, cytokinesis and ciliogenesis. Involved in the endosome-to-plasma membrane trafficking and recycling of SNX27-retromer-dependent cargo proteins, such as GLUT1. Involved in the regulation of cytokinesis; the function may involve PTPN13 and GIT1. Plays a role in the formation of cilia. Involved in cargo protein localization, such as PKD2, at primary cilia. 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.

Subunit / interactions. Found in a complex with ENTR1, PTPN13 and GIT1. Interacts with PTPN13 (via the FERM domain). Interacts (via N-terminus) with GIT1 (via N- and C-terminus); this interaction is direct. Interacts with NOD2. Interacts (via N-terminus) with IFT88. Interacts with VPS35.

Subcellular location. Cytoplasm. Early endosome. Endosome. Recycling endosome. Midbody. Cytoskeleton. Microtubule organizing center. Centrosome. Cilium basal body.

Tissue specificity. Expressed in the colon (at protein level).

Post-translational modifications. Phosphorylated.

Domain organisation. Tne N-terminal domain is necessary and sufficient for basal body localization and ciliogenesis.

Similarity. Belongs to the ENTR1 family.

Isoforms (4)

UniProt IDNamesCanonical?
Q96C92-11yes
Q96C92-22
Q96C92-33
Q96C92-44

RefSeq proteins (3): NP_001034796, NP_001034797, NP_006634 (=MANE)

Domains & families (InterPro)

IDNameType
IPR026757ENTR1Family

UniProt features (23 total): sequence variant 5, modified residue 4, region of interest 3, splice variant 3, mutagenesis site 2, sequence conflict 2, compositionally biased region 2, chain 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q96C92-F165.280.36

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (4): 247, 18, 147, 243

Mutagenesis-validated functional residues (2):

PositionPhenotype
190disrupts interaction with ptpn13.
194disrupts interaction with ptpn13.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 157 (showing top): GOBP_PROTEIN_LOCALIZATION_TO_CILIUM, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_UP, GOBP_POSITIVE_REGULATION_OF_PROTEIN_LOCALIZATION, ACEVEDO_NORMAL_TISSUE_ADJACENT_TO_LIVER_TUMOR_DN, GOBP_VESICLE_MEDIATED_TRANSPORT, GOBP_POSITIVE_REGULATION_OF_ORGANELLE_ORGANIZATION, GOBP_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, GOCC_MICROTUBULE_ORGANIZING_CENTER, GOBP_POSITIVE_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, GOBP_REGULATION_OF_CELL_PROJECTION_ORGANIZATION, FOSTER_TOLERANT_MACROPHAGE_UP, GOBP_CYTOKINESIS, BLALOCK_ALZHEIMERS_DISEASE_UP, GOBP_CILIUM_ORGANIZATION

GO Biological Process (7): protein transport (GO:0015031), cell projection organization (GO:0030030), endocytic recycling (GO:0032456), regulation of cytokinesis (GO:0032465), positive regulation of cilium assembly (GO:0045724), cell division (GO:0051301), positive regulation of protein localization to cilium (GO:1903566)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (10): endosome (GO:0005768), early endosome (GO:0005769), centrosome (GO:0005813), midbody (GO:0030496), ciliary basal body (GO:0036064), recycling endosome (GO:0055037), cytoplasm (GO:0005737), cytoskeleton (GO:0005856), retromer complex (GO:0030904), cell projection (GO:0042995)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure3
endomembrane system2
endosome2
microtubule organizing center2
transport1
intracellular protein localization1
establishment of protein localization1
cellular component organization1
endosomal transport1
vesicle-mediated transport to the plasma membrane1
cytokinesis1
regulation of cell cycle process1
regulation of cell division1
cilium assembly1
positive regulation of plasma membrane bounded cell projection assembly1
regulation of cilium assembly1
positive regulation of organelle assembly1
cellular process1
protein localization to cilium1
regulation of protein localization to cilium1
positive regulation of protein localization1
binding1
cytoplasmic vesicle1
centriole1
cilium1
intracellular anatomical structure1
intracellular membraneless organelle1
membrane protein complex1

Protein interactions and networks

STRING

702 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ENTR1PTPN13Q12923630
ENTR1ANKRD27Q96NW4581
ENTR1ANKRD50Q9ULJ7570
ENTR1GPSM1Q86YR5565
ENTR1CARD9Q9H257549
ENTR1VPS26AO75436545
ENTR1VPS26BQ4G0F5543
ENTR1VPS29Q9UBQ0533
ENTR1CENATACQ86UT8528
ENTR1NKX2-3Q8TAU0491
ENTR1SLC9A4Q6AI14490
ENTR1VPS35Q96QK1489
ENTR1TMEM69Q5SWH9477
ENTR1PTPN2P17706423
ENTR1CCP110O43303423
ENTR1SMC5Q8IY18423

IntAct

88 interactions, top by confidence:

ABTypeScore
MED4MED19psi-mi:“MI:2364”(proximity)0.900
ODAD1HGSpsi-mi:“MI:0914”(association)0.850
IFT88ENTR1psi-mi:“MI:0915”(physical association)0.600
ENTR1IFT88psi-mi:“MI:0403”(colocalization)0.600
NOD2ENTR1psi-mi:“MI:0915”(physical association)0.550
ENTR1NOD2psi-mi:“MI:0915”(physical association)0.550
NOD2ENTR1psi-mi:“MI:2364”(proximity)0.550
VPS35ENTR1psi-mi:“MI:0914”(association)0.530
NUP62RGPD8psi-mi:“MI:0914”(association)0.530
AURKAWDR62psi-mi:“MI:0914”(association)0.530
HSPA8ARHGEF10psi-mi:“MI:2364”(proximity)0.480
ENTR1PKMpsi-mi:“MI:0217”(phosphorylation reaction)0.440
GSK3BSEC16Apsi-mi:“MI:2364”(proximity)0.420
ENTR1psi-mi:“MI:0915”(physical association)0.400
ENTR1CSNK1Epsi-mi:“MI:0915”(physical association)0.370
ENTR1AP1M1psi-mi:“MI:0915”(physical association)0.370
OFD1SUPT5Hpsi-mi:“MI:0914”(association)0.350
Xpo1IFT56psi-mi:“MI:0914”(association)0.350
WRAP73AKAP8psi-mi:“MI:0914”(association)0.350
EGLN3FAM168Bpsi-mi:“MI:0914”(association)0.350
ORF2PRMT3psi-mi:“MI:0914”(association)0.350
TNIP2TMEM178Bpsi-mi:“MI:0914”(association)0.350
VPS35WASHC1psi-mi:“MI:0914”(association)0.350
VPS35ILVBLpsi-mi:“MI:0914”(association)0.350

BioGRID (250): SDCCAG3 (Two-hybrid), SDCCAG3 (Two-hybrid), SDCCAG3 (Two-hybrid), TFPT (Two-hybrid), SDCCAG3 (Affinity Capture-MS), SDCCAG3 (Affinity Capture-MS), SDCCAG3 (Proximity Label-MS), SDCCAG3 (Proximity Label-MS), SDCCAG3 (Proximity Label-MS), SDCCAG3 (Affinity Capture-MS), SDCCAG3 (Proximity Label-MS), SDCCAG3 (Proximity Label-MS), SDCCAG3 (Proximity Label-MS), SDCCAG3 (Proximity Label-MS), SDCCAG3 (Proximity Label-MS)

ESM2 similar proteins: A0FKI7, A2AHC3, A2AIW0, A4IH95, A5WUN7, A5WV69, A6H5Y1, A8MW92, D3Z8E6, P07106, P28290, P59598, Q08AD1, Q12912, Q2PFD7, Q3KQW7, Q4KLH6, Q4V9H5, Q502L1, Q52KN3, Q5R7V3, Q5REF4, Q5RHB5, Q5RJ80, Q5T5Y3, Q5T8D3, Q5XG73, Q5XI67, Q5ZHQ6, Q60664, Q640L3, Q640U0, Q641E3, Q6IRN6, Q6NPP4, Q6NRK3, Q6ZVD7, Q70EL1, Q76N89, Q8IX21

Diamond homologs: A2AIW0, A2CE83, Q28GJ0, Q2KJD6, Q54MB1, Q96C92

SIGNOR signaling

1 interactions.

AEffectBMechanism
SMURF1unknownENTR1ubiquitination

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 97 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
AURKA Activation by TPX21126.2×5e-11
Loss of Nlp from mitotic centrosomes1024.8×5e-10
Loss of proteins required for interphase microtubule organization from the centrosome1024.8×5e-10
Anchoring of the basal body to the plasma membrane1323.0×3e-12
Regulation of PLK1 Activity at G2/M Transition1121.8×3e-10
Recruitment of mitotic centrosome proteins and complexes1021.2×2e-09
Recruitment of NuMA to mitotic centrosomes1018.2×8e-09

GO biological processes:

GO termPartnersFoldFDR
centrosome duplication553.2×5e-06
centriole replication650.0×1e-06
non-motile cilium assembly619.8×8e-05
centrosome cycle519.1×5e-04
mitotic spindle organization515.4×9e-04
cilium assembly119.2×5e-06
intracellular protein localization67.1×6e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

147 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance112
Likely benign4
Benign3

Top pathogenic / likely-pathogenic (0)

SpliceAI

1935 predictions. Top by Δscore:

VariantEffectΔscore
9:136404048:CACT:Cdonor_loss1.0000
9:136404052:CACT:Cdonor_loss1.0000
9:136404053:A:ACdonor_gain1.0000
9:136404054:C:CCdonor_gain1.0000
9:136404054:CTTG:Cdonor_gain1.0000
9:136404083:C:CTdonor_gain1.0000
9:136404192:CGC:Cacceptor_gain1.0000
9:136404195:C:CCacceptor_gain1.0000
9:136404619:T:TAdonor_gain1.0000
9:136405035:T:Adonor_gain1.0000
9:136405061:G:Cdonor_gain1.0000
9:136405066:T:TAdonor_gain1.0000
9:136405089:A:ACdonor_gain1.0000
9:136405090:C:CCdonor_gain1.0000
9:136405090:CGGT:Cdonor_gain1.0000
9:136405199:CACC:Cacceptor_gain1.0000
9:136405200:ACC:Aacceptor_gain1.0000
9:136405201:CC:Cacceptor_gain1.0000
9:136405201:CCC:Cacceptor_gain1.0000
9:136405202:CC:Cacceptor_gain1.0000
9:136405202:CCT:Cacceptor_loss1.0000
9:136405203:C:CCacceptor_gain1.0000
9:136405203:C:Tacceptor_gain1.0000
9:136405204:T:Cacceptor_gain1.0000
9:136405204:T:TCacceptor_gain1.0000
9:136405207:T:Cacceptor_gain1.0000
9:136405207:T:TCacceptor_gain1.0000
9:136405899:A:ACdonor_gain1.0000
9:136405900:C:CCdonor_gain1.0000
9:136405900:CATA:Cdonor_gain1.0000

AlphaMissense

2834 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
9:136404687:C:GA338P0.994
9:136404678:C:GA341P0.993
9:136405104:A:GL331P0.993
9:136402840:A:GL419P0.990
9:136405956:A:GL281P0.990
9:136404091:A:GL391P0.988
9:136404656:A:GL348P0.987
9:136405094:C:AM334I0.985
9:136405094:C:GM334I0.985
9:136405094:C:TM334I0.985
9:136407901:G:CF109L0.984
9:136407901:G:TF109L0.984
9:136407903:A:GF109L0.984
9:136405944:A:GL285P0.982
9:136402835:A:GS421P0.981
9:136402882:A:GL405P0.980
9:136405191:A:GL302P0.980
9:136404686:G:TA338D0.979
9:136404689:C:GR337P0.978
9:136407886:A:CF114L0.978
9:136407886:A:TF114L0.978
9:136407888:A:GF114L0.978
9:136402840:A:TL419H0.975
9:136405125:A:TV324D0.975
9:136405977:A:GL274P0.975
9:136407895:A:CF111L0.975
9:136407895:A:TF111L0.975
9:136407897:A:GF111L0.975
9:136404635:A:GL355P0.973
9:136405185:C:GR304P0.971

dbSNP variants (sampled 300 via entrez): RS1000280431 (9:136412300 C>A,T), RS1000479449 (9:136412286 A>G), RS1000840705 (9:136408835 G>A), RS1001086175 (9:136405253 G>A), RS1001131871 (9:136411208 C>G,T), RS1001140211 (9:136405464 G>A), RS1001356846 (9:136408977 A>G), RS1001711887 (9:136405219 C>A,T), RS1002343741 (9:136408654 T>C), RS1002711292 (9:136411608 G>A), RS1003093233 (9:136408710 G>A), RS1003099807 (9:136407072 T>C), RS1003144289 (9:136408823 T>C), RS1003309045 (9:136405638 A>G), RS1003489624 (9:136407933 T>C)

Disease associations

OMIM: gene MIM:618289 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

8 associations (top):

StudyTraitp-value
GCST000964_39Ulcerative colitis3.000000e-19
GCST001725_102Inflammatory bowel disease4.000000e-56
GCST004131_21Inflammatory bowel disease5.000000e-36
GCST004132_11Crohn’s disease6.000000e-30
GCST004133_17Ulcerative colitis2.000000e-16
GCST008643_2Joint damage in rheumatoid arthritis1.000000e-06
GCST90020028_33Hip circumference adjusted for BMI4.000000e-08
GCST90020028_34Hip circumference adjusted for BMI5.000000e-09

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0005413joint damage measurement
EFO:0008039BMI-adjusted hip circumference

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

26 total (human), top 26 by PubMed support.

ChemicalActions (top 5)PubMed papers
cobaltous chloridedecreases expression2
Acetaminophenincreases expression, affects response to substance2
Valproic Aciddecreases expression, increases methylation2
Cadmium Chloridedecreases expression, increases expression2
aristolochic acid Iincreases expression1
FR900359decreases phosphorylation1
bufotalindecreases expression1
sodium arsenitedecreases expression1
coumarindecreases phosphorylation1
di-n-butylphosphoric acidaffects expression1
Temozolomideincreases expression1
Sunitinibincreases expression1
Vehicle Emissionsdecreases expression, increases abundance1
Doxorubicindecreases expression1
Enzyme Inhibitorsdecreases activity, increases O-linked glycosylation1
Estradiolincreases expression1
Hydrogen Peroxideaffects expression1
Nickelincreases expression1
Silicon Dioxideincreases expression1
Smokedecreases expression1
Thiramdecreases expression1
Tobacco Smoke Pollutionincreases expression1
Metriboloneincreases expression1
Sodium Seleniteincreases expression1
Copper Sulfatedecreases expression1
Particulate Matterdecreases expression, increases abundance1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.