ENTPD3-AS1

Summary

ENTPD3-AS1 (ENTPD3, EIF1B and MYRIP antisense RNA 1, HGNC:26710) is a long non-coding RNA gene on chromosome 3p22.1.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 118 total

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26710
Approved symbol	ENTPD3-AS1
Name	ENTPD3, EIF1B and MYRIP antisense RNA 1
Location	3p22.1
Locus type	RNA, long non-coding
Status	Approved
Aliases	FLJ36665
Ensembl gene	ENSG00000223797
Entrez	285266
RNAcentral	URS000075F091 — lncRNA, 2039 nt, 1 organism(s)

Gene structure

Transcript identifiers

Ensembl transcripts: 0

RefSeq mRNA: 0 — MANE Select: None

Canonical transcript exons

None — 0 exons

Expression profiles

Bgee: expression breadth ubiquitous, 167 present calls, max score 83.37.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 1.9107 / max 32.8607, expressed in 963 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
41758	1.9107	963

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	83.37	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	79.39	gold quality
hindlimb stylopod muscle	UBERON:0004252	77.75	gold quality
spinal cord	UBERON:0002240	76.04	gold quality
islet of Langerhans	UBERON:0000006	75.75	gold quality
sural nerve	UBERON:0015488	75.34	gold quality
calcaneal tendon	UBERON:0003701	75.32	gold quality
right lobe of liver	UBERON:0001114	74.86	gold quality
muscle of leg	UBERON:0001383	74.61	gold quality
right adrenal gland	UBERON:0001233	74.24	gold quality
right adrenal gland cortex	UBERON:0035827	74.01	gold quality
gastrocnemius	UBERON:0001388	73.92	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	73.73	gold quality
left adrenal gland cortex	UBERON:0035825	72.83	gold quality
left adrenal gland	UBERON:0001234	72.81	gold quality
adult mammalian kidney	UBERON:0000082	72.78	gold quality
right uterine tube	UBERON:0001302	72.69	gold quality
colonic epithelium	UBERON:0000397	72.43	gold quality
amygdala	UBERON:0001876	71.94	gold quality
putamen	UBERON:0001874	71.75	gold quality
anterior cingulate cortex	UBERON:0009835	71.73	gold quality
prefrontal cortex	UBERON:0000451	71.47	gold quality
hypothalamus	UBERON:0001898	71.07	gold quality
adrenal cortex	UBERON:0001235	70.80	gold quality
pancreas	UBERON:0001264	70.80	gold quality
adrenal gland	UBERON:0002369	70.75	gold quality
tibial nerve	UBERON:0001323	70.69	gold quality
popliteal artery	UBERON:0002250	70.47	gold quality
tibial artery	UBERON:0007610	70.47	gold quality
Brodmann (1909) area 9	UBERON:0013540	70.28	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.32

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 1)

• SNP-mediated lncRNA-ENTPD3-AS1 upregulation suppresses renal cell carcinoma via miR-155/HIF-1alpha signaling. (PMID:34218253)

Cross-species orthologs

0 orthologs

Protein

Protein identifiers

Canonical reviewed UniProt: None (reviewed: )

All UniProt accessions (0):

RefSeq proteins (0): (*=MANE)

Domains & families (InterPro)

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 22 (showing top): chr3p22, DODD_NASOPHARYNGEAL_CARCINOMA_DN, HHEX_TARGET_GENES, KAT2A_TARGET_GENES, NAB2_TARGET_GENES, NFE2L1_TARGET_GENES, SFMBT1_TARGET_GENES, TAFAZZIN_TARGET_GENES, ZNF407_TARGET_GENES, ZNF618_TARGET_GENES, ZNF768_TARGET_GENES, GSE13738_RESTING_VS_BYSTANDER_ACTIVATED_CD4_TCELL_UP, ZSCAN5DP_TARGET_GENES, BRCA2_TARGET_GENES, HARALAMBIEVA_PBMC_FLUARIX_AGE_50_74YO_CORR_WITH_28D_MEM_B_CELL_RESPONSE_AT_3DY_NEGATIVE

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

0 interactions, top by confidence (×1000):

IntAct

0 interactions, top by confidence:

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	99
Likely benign	5
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

5032 predictions. Top by Δscore:

Variant	Effect	Δscore
3:40151046:A:AG	acceptor_gain	1.0000
3:40151046:AGG:A	acceptor_loss	1.0000
3:40151047:G:GA	acceptor_loss	1.0000
3:40151047:G:GG	acceptor_gain	1.0000
3:40151144:G:GT	donor_gain	1.0000
3:40151186:T:G	donor_loss	1.0000
3:40166841:TCTA:T	acceptor_loss	1.0000
3:40166842:CTA:C	acceptor_loss	1.0000
3:40166843:TAGG:T	acceptor_loss	1.0000
3:40166844:A:G	acceptor_loss	1.0000
3:40166905:G:GT	donor_gain	1.0000
3:40166926:GCA:G	donor_gain	1.0000
3:40166939:GCCTG:G	donor_gain	1.0000
3:40166941:CTGGT:C	donor_loss	1.0000
3:40166942:TGGT:T	donor_loss	1.0000
3:40166943:GGT:G	donor_loss	1.0000
3:40166944:GTAGG:G	donor_loss	1.0000
3:40166945:T:A	donor_loss	1.0000
3:40167157:A:AG	acceptor_gain	1.0000
3:40167157:AG:A	acceptor_gain	1.0000
3:40167157:AGGA:A	acceptor_loss	1.0000
3:40167158:G:GA	acceptor_gain	1.0000
3:40167158:GG:G	acceptor_gain	1.0000
3:40167158:GGA:G	acceptor_gain	1.0000
3:40167158:GGAC:G	acceptor_gain	1.0000
3:40167158:GGACA:G	acceptor_gain	1.0000
3:40167236:GAAG:G	donor_gain	1.0000
3:40167238:AGG:A	donor_loss	1.0000
3:40167240:G:GG	donor_gain	1.0000
3:40169946:CCA:C	acceptor_loss	1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000012181 (3:40427114 G>A), RS1000019235 (3:40407201 G>A), RS1000035189 (3:40423739 A>T), RS1000075095 (3:40393239 T>C), RS1000108548 (3:40423484 G>A), RS1000302418 (3:40417660 C>T), RS1000339074 (3:40439947 GA>G,GAA), RS1000359170 (3:40404160 A>G), RS1000371744 (3:40439494 CA>C,CAA), RS1000413919 (3:40410468 A>G), RS1000436215 (3:40453712 T>C), RS1000563227 (3:40448935 C>T), RS1000578796 (3:40433312 T>A,C), RS1000674079 (3:40394790 G>A,C), RS1000709196 (3:40404534 G>A)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (1): prostate cancer (MONDO:0008315)

Orphanet (1): Familial prostate cancer (Orphanet:1331)

HPO phenotypes

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

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST009200_3	Whole brain grey matter density	7.000000e-06
GCST90002382_561	Eosinophil percentage of white cells	2.000000e-09

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0010306	Grey matter density measurement
EFO:0007991	eosinophil percentage of leukocytes

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
D011471	Prostatic Neoplasms	C04.588.945.440.770; C12.100.500.260.750; C12.100.500.565.625; C12.200.294.260.750; C12.200.294.565.625; C12.200.758.409.750; C12.900.619.750

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 0 entries

CTD chemical–gene interactions

11 total (human), top 11 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression	2
fipronil	affects cotreatment, decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
jinfukang	increases expression	1
2,3,5-trichloro-6-phenyl-(1,4)benzoquinone	increases expression	1
DEET	affects cotreatment, decreases expression	1
Methotrexate	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Okadaic Acid	decreases expression	1
Acrylamide	increases expression	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT00029224	PHASE4	COMPLETED	Treatment With Zoledronic Acid in Patients With Breast Cancer, Multiple Myeloma, and Prostate Cancer With Cancer Related Bone Lesions
NCT00035997	PHASE4	COMPLETED	Open-label Trial on the Effect of I.V. Zoledronic Acid 4 mg on Bone Density in Hormone Sensitive Prostate Cancer Patients With Bone Metastasis
NCT00063609	PHASE4	COMPLETED	The Effect of Zoledronic Acid on Bone Loss in Prostate Cancer Patients Undergoing Androgen Deprivation Therapy
NCT00103623	PHASE4	SUSPENDED	The Plenaxis® Experience Study
NCT00106392	PHASE4	COMPLETED	A Safety and Efficacy Study of Prograf in the Prevention of Erectile Dysfunction After Radical Prostatectomy
NCT00185029	PHASE4	UNKNOWN	MR-Lymphography and Lymph Node Staging in Prostate Cancer
NCT00199485	PHASE4	COMPLETED	Angelica Sinensis for the Treatment of Hot Flashes in Men Undergoing LHRH Therapy for Prostate Cancer
NCT00219219	PHASE4	COMPLETED	Zoledronic Acid in the Prevention of Skeletal-related Events in Hormone Refractory and Hormone-sensitive Prostate Cancer Patients With Bone Metastases
NCT00219271	PHASE4	COMPLETED	Effect Of Zoledronic Acid On Circulating And Bone Marrow-Residing Prostate Cancer Cells In Patients With Clinically Localized Prostate Cancer
NCT00237146	PHASE4	COMPLETED	Study to Evaluate Zoledronic Acid on Quality of Life and Skeletal-related Events as Adjuvant Treatment in Patients With Hormone-naïve Prostate Cancer and Bone Metastasis Who Have Undergone Orchiectomy
NCT00242554	PHASE4	COMPLETED	Open-label Phase IV Clinical Trial to Evaluate the Safety and Tolerability of Zoledronic Acid in Patients With Prostate Cancer and Bone Metastases
NCT00280098	PHASE4	COMPLETED	Docetaxel in the Treatment of Hormone Refractory Prostate Cancer
NCT00293696	PHASE4	COMPLETED	Casodex/Zoladex Biomarkers in Localised Prostate Cancer
NCT00334139	PHASE4	COMPLETED	Effect of Zoledronic Acid on Bone Metabolism in Patients With Bone Metastasis and Prostate or Breast Cancer
NCT00375765	PHASE4	COMPLETED	Effects On Dihydrotestosterone Regulated Gene Expression In Benign Prostatic Hyperplasia Or Prostate Cancer
NCT00391690	PHASE4	COMPLETED	Evaluation of Bone Markers as Diagnostic Tools for Early Detection of Bone Metastases in Patients With High Risk Prostate Cancer
NCT00422708	PHASE4	COMPLETED	Local Anesthesia for Prostate Biopsy
NCT00526331	PHASE4	COMPLETED	Evaluation of Arterial Pressure Based Cardiac Output for Goal-Directed Perioperative Therapy
NCT00590213	PHASE4	COMPLETED	Compare the Value of Prophylactic Versus Therapeutic Breast Radiotherapy in CASODEX
NCT00629330	PHASE4	TERMINATED	Dissemination of Prostate Cancer Screening to PCP’s in African American Communities
NCT00771966	PHASE4	COMPLETED	Radical Prostatectomy and Perioperative Fluid Therapy
NCT00805701	PHASE4	COMPLETED	Study Assessing The Efficacy And Safety Of Avodart (Dutasteride) At Improving Urinary Symptoms In Men With Prostate Cancer Who Are Undergoing Seed Implantation
NCT00859027	PHASE4	COMPLETED	Effect Of Risedronate On Bone Mass In Older Men Receiving Neoadjuvant Therapy For Prostate Cancer
NCT00906269	PHASE4	UNKNOWN	Can Hyperbaric Oxygen Improve Erectile Function Following Surgery for Prostate Cancer
NCT00953277	PHASE4	COMPLETED	Study of Nerve Reconstruction Using AVANCE in Subjects Who Undergo Robotic Assisted Prostatectomy for Treatment of Prostate Cancer
NCT00982800	PHASE4	COMPLETED	Does Postoperative Gabapentin Reduce Pain, Opioid Consumption and Anxiety and Have a Positive Effect on Health Related Quality of Life After Radical Prostatectomy?
NCT01083199	PHASE4	COMPLETED	Global Performance Evaluation of the AMS CONTINUUM™ Device
NCT01136226	PHASE4	COMPLETED	Evaluate Recovery of Testosterone for Patients Using Eligard
NCT01161563	PHASE4	COMPLETED	Randomized Crossover Trial to Assess the Tolerability of Gonadotropin Releasing Hormone (GnRH) Analogue Administration
NCT01230905	PHASE4	COMPLETED	Study to Monitor the Effects of Androgen Suppression Treatment on the Heart
NCT01296672	PHASE4	COMPLETED	3 Month Finasteride Challenge Test Can Significantly Improve the Performance of Screening for Prostate Cancer
NCT01365143	PHASE4	TERMINATED	Prospective Randomized Trial Comparing Robotic Versus Open Radical Prostatectomy
NCT01379742	PHASE4	UNKNOWN	Comparison of Between ThinSeed™ and OncoSeed™ for Permanent Prostate Brachytherapy
NCT01486563	PHASE4	COMPLETED	Hydroxyethyl Starch and Renal Function After Radical Prostatectomy
NCT01511874	PHASE4	COMPLETED	Efficacy and Safety Study of ELIGARD 22.5mg With Prostate Cancer
NCT01512472	PHASE4	TERMINATED	Firmagon (Degarelix) Intermittent Therapy
NCT01547416	PHASE4	COMPLETED	The Effect of Combined General/Epidural Anesthesia Versus General Anesthesia on Diaphragmatic Function
NCT01571544	PHASE4	COMPLETED	The Use of Thermal Suits as Preventing Hypothermia During Surgery
NCT01581749	PHASE4	UNKNOWN	Evaluation of Truebeam for Low-Intermediate Risk Prostate Cancer
NCT01649635	PHASE4	COMPLETED	Study of Cabazitaxel Combined With Prednisone and Prophylaxis of Neutropenia Complications in the Treatment of Patients With Metastatic Castration-resistant Prostate Cancer