RPUSD1

gene
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Also known as RLUCLMGC19600

Summary

RPUSD1 (RNA pseudouridine synthase domain containing 1, HGNC:14173) is a protein-coding gene on chromosome 16p13.3, encoding RNA pseudouridylate synthase domain-containing protein 1 (Q9UJJ7).

Predicted to enable pseudouridine synthase activity. Predicted to be involved in enzyme-directed rRNA pseudouridine synthesis.

Source: NCBI Gene 113000 — RefSeq curated summary.

At a glance

  • GWAS associations: 1
  • Clinical variants (ClinVar): 102 total
  • MANE Select transcript: NM_058192

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:14173
Approved symbolRPUSD1
NameRNA pseudouridine synthase domain containing 1
Location16p13.3
Locus typegene with protein product
StatusApproved
AliasesRLUCL, MGC19600
Ensembl geneENSG00000007376
Ensembl biotypeprotein_coding
Entrez113000

Gene structure

Transcript identifiers

Ensembl transcripts: 14 — 12 protein_coding, 2 nonsense_mediated_decay

ENST00000007264, ENST00000561734, ENST00000562070, ENST00000563560, ENST00000565377, ENST00000565503, ENST00000565809, ENST00000567114, ENST00000567283, ENST00000569601, ENST00000918138, ENST00000918139, ENST00000947984, ENST00000947985

RefSeq mRNA: 11 — MANE Select: NM_058192 NM_001324086, NM_001324410, NM_001324411, NM_001324412, NM_001324413, NM_001324414, NM_001324415, NM_001369658, NM_001369659, NM_001369660, NM_058192

CCDS: CCDS10426, CCDS81923, CCDS81924

Canonical transcript exons

ENST00000007264 — 6 exons

ExonStartEnd
ENSE00001062022784974786377
ENSE00001118601787556787744
ENSE00002589006788256788381
ENSE00003532997787354787477
ENSE00003611069786827786928
ENSE00003622015787077787179

Expression profiles

Bgee: expression breadth ubiquitous, 205 present calls, max score 90.49.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 16.1990 / max 83.1444, expressed in 1799 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
15578516.19901799

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
pancreatic ductal cellCL:000207990.49silver quality
granulocyteCL:000009488.93gold quality
mucosa of transverse colonUBERON:000499188.62gold quality
ileal mucosaUBERON:000033187.22silver quality
right frontal lobeUBERON:000281086.95gold quality
upper arm skinUBERON:000426386.91gold quality
tibialis anteriorUBERON:000138586.00silver quality
lower esophagus mucosaUBERON:003583485.75gold quality
prefrontal cortexUBERON:000045185.70gold quality
anterior cingulate cortexUBERON:000983585.58gold quality
monocyteCL:000057685.36gold quality
Brodmann (1909) area 9UBERON:001354085.30gold quality
leukocyteCL:000073885.26gold quality
body of stomachUBERON:000116184.61gold quality
right hemisphere of cerebellumUBERON:001489084.45gold quality
apex of heartUBERON:000209884.40gold quality
spleenUBERON:000210684.19gold quality
metanephros cortexUBERON:001053383.71gold quality
skin of legUBERON:000151183.44gold quality
frontal cortexUBERON:000187083.34gold quality
neocortexUBERON:000195083.31gold quality
esophagus mucosaUBERON:000246983.28gold quality
transverse colonUBERON:000115783.20gold quality
dorsolateral prefrontal cortexUBERON:000983483.16gold quality
cerebellar hemisphereUBERON:000224582.96gold quality
putamenUBERON:000187482.89gold quality
cerebellar cortexUBERON:000212982.86gold quality
skin of abdomenUBERON:000141682.23gold quality
small intestine Peyer’s patchUBERON:000345482.22gold quality
bloodUBERON:000017882.19gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

ExperimentMarker?Max mean expression
E-ANND-3no2.32

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

23 targeting RPUSD1, 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-520G-5P99.9966.76658
HSA-MIR-6870-5P99.9968.552115
HSA-MIR-4723-5P99.9768.702034
HSA-MIR-569899.9768.492029
HSA-MIR-7111-5P99.9768.482062
HSA-MIR-452599.9464.38675
HSA-MIR-5010-5P99.9464.11705
HSA-MIR-182799.6368.573265
HSA-MIR-127599.4767.902749
HSA-MIR-797499.2465.481137
HSA-MIR-625-5P99.0268.642031
HSA-MIR-3619-5P99.0068.872308
HSA-MIR-214-3P98.7168.122128
HSA-MIR-76198.7168.072051
HSA-MIR-423-5P98.6967.481522
HSA-MIR-3184-5P98.5667.131491
HSA-MIR-6827-5P98.4664.881256
HSA-MIR-5008-5P98.4265.871019
HSA-MIR-66597.6065.641781
HSA-MIR-505-5P97.0165.54778
HSA-MIR-390796.7665.04662
HSA-MIR-286195.2465.471056
HSA-MIR-6786-3P93.7360.7052

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriorpusd1ENSDARG00000060192
mus_musculusRpusd1ENSMUSG00000041199
rattus_norvegicusRpusd1ENSRNOG00000023639

Paralogs (3): RPUSD3 (ENSG00000156990), RPUSD4 (ENSG00000165526), RPUSD2 (ENSG00000166133)

Protein

Protein identifiers

RNA pseudouridylate synthase domain-containing protein 1Q9UJJ7 (reviewed: Q9UJJ7)

Alternative names: Ribosomal large subunit pseudouridine synthase C-like protein

All UniProt accessions (9): Q9UJJ7, H3BMZ6, H3BQN8, H3BRG3, H3BS55, H3BSG4, H3BU91, H3BUN6, H3BVD0

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the pseudouridine synthase RluA family.

RefSeq proteins (11): NP_001311015, NP_001311339, NP_001311340, NP_001311341, NP_001311342, NP_001311343, NP_001311344, NP_001356587, NP_001356588, NP_001356589, NP_478072* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR006145PsdUridine_synth_RsuA/RluADomain
IPR020103PsdUridine_synth_cat_dom_sfHomologous_superfamily
IPR050188RluA_PseudoU_synthaseFamily

Pfam: PF00849

UniProt features (29 total): strand 15, helix 4, turn 3, sequence variant 2, chain 1, region of interest 1, compositionally biased region 1, active site 1, modified residue 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
5VBBX-RAY DIFFRACTION1.94

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9UJJ7-F186.850.74

Functional residue map

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

Catalytic / active sites (1): 67

Post-translational modifications (1): 1

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 74 (showing top): GSE45365_NK_CELL_VS_CD11B_DC_UP, GOBP_RIBOSOME_BIOGENESIS, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GOBP_PSEUDOURIDINE_SYNTHESIS, GOBP_RNA_MODIFICATION, MODULE_397, GOBP_RRNA_MODIFICATION, GOBP_RIBONUCLEOPROTEIN_COMPLEX_BIOGENESIS, MARSON_BOUND_BY_E2F4_UNSTIMULATED, NIKOLSKY_BREAST_CANCER_16P13_AMPLICON, GOMF_PSEUDOURIDINE_SYNTHASE_ACTIVITY, GOMF_INTRAMOLECULAR_TRANSFERASE_ACTIVITY, GOMF_ISOMERASE_ACTIVITY, LU_EZH2_TARGETS_UP, BHAT_ESR1_TARGETS_NOT_VIA_AKT1_UP

GO Biological Process (3): enzyme-directed rRNA pseudouridine synthesis (GO:0000455), pseudouridine synthesis (GO:0001522), RNA modification (GO:0009451)

GO Molecular Function (3): RNA binding (GO:0003723), pseudouridine synthase activity (GO:0009982), protein binding (GO:0005515)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
rRNA pseudouridine synthesis1
RNA modification1
RNA metabolic process1
macromolecule modification1
nucleic acid binding1
intramolecular transferase activity1
binding1

Protein interactions and networks

STRING

1589 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
RPUSD1RPUSD3Q6P087795
RPUSD1PUS7LQ9H0K6793
RPUSD1PUS3Q9BZE2766
RPUSD1PUS10Q3MIT2744
RPUSD1PUS1Q9Y606724
RPUSD1TRUB2O95900707
RPUSD1PUS7Q96PZ0663
RPUSD1TRUB1Q8WWH5654
RPUSD1PUSL1Q8N0Z8608
RPUSD1CHTF18Q8WVB6507
RPUSD1DCTN5Q9BTE1488
RPUSD1DKC1O60832469
RPUSD1NOP10Q9NPE3413
RPUSD1THUMPD2Q9BTF0410
RPUSD1INAFM1C9JVW0407

IntAct

10 interactions, top by confidence:

ABTypeScore
SPRED1RPUSD1psi-mi:“MI:0915”(physical association)0.560
HNRNPCL2RPUSD1psi-mi:“MI:0915”(physical association)0.400
RPUSD1FOXJ1psi-mi:“MI:0915”(physical association)0.370
Tnks2AMOTL2psi-mi:“MI:0914”(association)0.350
Klhl21DERL1psi-mi:“MI:0914”(association)0.350
Ankfy1ANXA2psi-mi:“MI:0914”(association)0.350
PTENDNAAF8psi-mi:“MI:0914”(association)0.350

BioGRID (8): RPUSD1 (Affinity Capture-MS), RPUSD1 (Affinity Capture-MS), RPUSD1 (Affinity Capture-MS), RPUSD1 (Affinity Capture-RNA), RPUSD1 (Proximity Label-MS), RPUSD1 (Affinity Capture-MS), RPUSD1 (Affinity Capture-MS), RPUSD1 (Two-hybrid)

ESM2 similar proteins: A2RT67, A2RUS2, A3BN26, A4PCD4, A5PKL6, E9PYK3, F1ND48, O75616, P04053, P06526, P09838, P36195, P42118, Q08C69, Q0DST9, Q149F1, Q14AI6, Q17QT4, Q28C59, Q2TBK7, Q3U269, Q3U3W5, Q49MI3, Q4QQT0, Q4R6Y8, Q5E9Z1, Q5EBA0, Q5M721, Q5M934, Q5RL51, Q61846, Q66KI9, Q6DBR0, Q6P087, Q8BGG7, Q8IZ73, Q8NEC7, Q8TF42, Q8VCZ8, Q92089

Diamond homologs: O16686, O25114, O25441, O25610, O66114, O67638, P0A5T3, P0AA37, P0AA38, P0AA41, P0AA42, P33640, P43930, P44197, P44433, P45614, P47451, P53294, P57430, P59831, P59840, P70870, P74346, P75485, P9WHQ2, P9WHQ3, Q08C69, Q0DST9, Q12069, Q149F1, Q17QT4, Q1RJX7, Q3ECD0, Q45480, Q45826, Q47417, Q4QQT0, Q4UKQ3, Q5M721, Q68XB2

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance89
Likely benign6
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

850 predictions. Top by Δscore:

VariantEffectΔscore
16:786826:C:CAdonor_gain1.0000
16:786839:T:TAdonor_gain1.0000
16:787075:AC:Adonor_gain1.0000
16:787076:C:CAdonor_gain1.0000
16:787348:TCTTA:Tdonor_loss1.0000
16:787351:TA:Tdonor_loss1.0000
16:787352:A:ACdonor_gain1.0000
16:787353:C:CCdonor_gain1.0000
16:787475:AACC:Aacceptor_loss1.0000
16:787476:ACC:Aacceptor_loss1.0000
16:787478:C:CCacceptor_gain1.0000
16:787550:CCCTA:Cdonor_loss1.0000
16:787551:CCTAC:Cdonor_loss1.0000
16:787552:CTAC:Cdonor_loss1.0000
16:787553:TACCT:Tdonor_loss1.0000
16:787554:ACCTG:Adonor_loss1.0000
16:787555:C:Gdonor_loss1.0000
16:787567:G:Cdonor_gain1.0000
16:786373:CCGGC:Cacceptor_gain0.9900
16:786374:CGGC:Cacceptor_gain0.9900
16:786374:CGGCC:Cacceptor_gain0.9900
16:786377:CCT:Cacceptor_loss0.9900
16:786378:C:CCacceptor_gain0.9900
16:786378:CTGCG:Cacceptor_loss0.9900
16:786379:T:Cacceptor_loss0.9900
16:786822:CACA:Cdonor_loss0.9900
16:786825:A:ACdonor_gain0.9900
16:786825:A:Tdonor_loss0.9900
16:786825:AC:Adonor_gain0.9900
16:786826:C:CCdonor_gain0.9900

AlphaMissense

2007 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
16:787460:T:AD67V0.999
16:786374:C:GR172P0.998
16:787369:C:AK97N0.998
16:787369:C:GK97N0.998
16:787459:A:CD67E0.998
16:787459:A:TD67E0.998
16:786369:G:CH174D0.997
16:787447:G:CS71R0.997
16:787447:G:TS71R0.997
16:787449:T:GS71R0.997
16:787460:T:CD67G0.997
16:787460:T:GD67A0.997
16:787669:C:AK23N0.997
16:787669:C:GK23N0.997
16:786364:C:AQ175H0.996
16:786364:C:GQ175H0.996
16:786367:G:CH174Q0.996
16:786367:G:TH174Q0.996
16:786377:C:TG171D0.996
16:787471:G:CC63W0.996
16:787472:C:TC63Y0.996
16:787558:G:CF60L0.996
16:787558:G:TF60L0.996
16:787559:A:GF60S0.996
16:787560:A:GF60L0.996
16:786275:C:AR205I0.995
16:786275:C:GR205T0.995
16:786349:G:CC180W0.995
16:786360:G:TR177S0.995
16:786841:A:GL166P0.995

dbSNP variants (sampled 300 via entrez): RS1000261081 (16:789879 G>A,T), RS1001515157 (16:789743 T>C,G), RS1001808659 (16:785547 C>A), RS1002088427 (16:784826 G>C), RS1002519499 (16:789180 C>A,G,T), RS1003350822 (16:788556 A>G), RS1003490214 (16:787852 G>A,C), RS1003736480 (16:787981 C>G,T), RS1004452143 (16:788853 G>A,C,T), RS1005185971 (16:785314 C>T), RS1005259565 (16:785406 C>A,T), RS1005508792 (16:785134 G>A), RS1005890644 (16:784657 G>A,T), RS1006193334 (16:784715 G>A,C,T), RS1006248045 (16:787866 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

1 associations (top):

StudyTraitp-value
GCST005951_12Body mass index5.000000e-11

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0004340body mass index

MeSH disease descriptors (1)

DescriptorNameTree numbers
D011471Prostatic NeoplasmsC04.588.945.440.770; 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: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

15 total (human), top 15 by PubMed support.

ChemicalActions (top 5)PubMed papers
sodium arseniteincreases expression, decreases expression2
triphenyl phosphateaffects expression1
abrinedecreases expression1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic aciddecreases expression1
Temozolomideincreases expression1
Benzo(a)pyreneaffects methylation, increases methylation1
Cadmiumincreases expression1
Doxorubicindecreases expression1
Estradiolincreases expression1
Selenomethionineaffects expression1
Thiramdecreases expression1
Tobacco Smoke Pollutionincreases expression1
Valproic Acidincreases methylation1
Aflatoxin B1increases methylation1
Sodium Seleniteincreases expression1

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT00029224PHASE4COMPLETEDTreatment With Zoledronic Acid in Patients With Breast Cancer, Multiple Myeloma, and Prostate Cancer With Cancer Related Bone Lesions
NCT00035997PHASE4COMPLETEDOpen-label Trial on the Effect of I.V. Zoledronic Acid 4 mg on Bone Density in Hormone Sensitive Prostate Cancer Patients With Bone Metastasis
NCT00063609PHASE4COMPLETEDThe Effect of Zoledronic Acid on Bone Loss in Prostate Cancer Patients Undergoing Androgen Deprivation Therapy
NCT00103623PHASE4SUSPENDEDThe Plenaxis® Experience Study
NCT00106392PHASE4COMPLETEDA Safety and Efficacy Study of Prograf in the Prevention of Erectile Dysfunction After Radical Prostatectomy
NCT00185029PHASE4UNKNOWNMR-Lymphography and Lymph Node Staging in Prostate Cancer
NCT00199485PHASE4COMPLETEDAngelica Sinensis for the Treatment of Hot Flashes in Men Undergoing LHRH Therapy for Prostate Cancer
NCT00219219PHASE4COMPLETEDZoledronic Acid in the Prevention of Skeletal-related Events in Hormone Refractory and Hormone-sensitive Prostate Cancer Patients With Bone Metastases
NCT00219271PHASE4COMPLETEDEffect Of Zoledronic Acid On Circulating And Bone Marrow-Residing Prostate Cancer Cells In Patients With Clinically Localized Prostate Cancer
NCT00237146PHASE4COMPLETEDStudy 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
NCT00242554PHASE4COMPLETEDOpen-label Phase IV Clinical Trial to Evaluate the Safety and Tolerability of Zoledronic Acid in Patients With Prostate Cancer and Bone Metastases
NCT00280098PHASE4COMPLETEDDocetaxel in the Treatment of Hormone Refractory Prostate Cancer
NCT00293696PHASE4COMPLETEDCasodex/Zoladex Biomarkers in Localised Prostate Cancer
NCT00334139PHASE4COMPLETEDEffect of Zoledronic Acid on Bone Metabolism in Patients With Bone Metastasis and Prostate or Breast Cancer
NCT00375765PHASE4COMPLETEDEffects On Dihydrotestosterone Regulated Gene Expression In Benign Prostatic Hyperplasia Or Prostate Cancer
NCT00391690PHASE4COMPLETEDEvaluation of Bone Markers as Diagnostic Tools for Early Detection of Bone Metastases in Patients With High Risk Prostate Cancer
NCT00422708PHASE4COMPLETEDLocal Anesthesia for Prostate Biopsy
NCT00526331PHASE4COMPLETEDEvaluation of Arterial Pressure Based Cardiac Output for Goal-Directed Perioperative Therapy
NCT00590213PHASE4COMPLETEDCompare the Value of Prophylactic Versus Therapeutic Breast Radiotherapy in CASODEX
NCT00629330PHASE4TERMINATEDDissemination of Prostate Cancer Screening to PCP’s in African American Communities
NCT00771966PHASE4COMPLETEDRadical Prostatectomy and Perioperative Fluid Therapy
NCT00805701PHASE4COMPLETEDStudy Assessing The Efficacy And Safety Of Avodart (Dutasteride) At Improving Urinary Symptoms In Men With Prostate Cancer Who Are Undergoing Seed Implantation
NCT00859027PHASE4COMPLETEDEffect Of Risedronate On Bone Mass In Older Men Receiving Neoadjuvant Therapy For Prostate Cancer
NCT00906269PHASE4UNKNOWNCan Hyperbaric Oxygen Improve Erectile Function Following Surgery for Prostate Cancer
NCT00953277PHASE4COMPLETEDStudy of Nerve Reconstruction Using AVANCE in Subjects Who Undergo Robotic Assisted Prostatectomy for Treatment of Prostate Cancer
NCT00982800PHASE4COMPLETEDDoes Postoperative Gabapentin Reduce Pain, Opioid Consumption and Anxiety and Have a Positive Effect on Health Related Quality of Life After Radical Prostatectomy?
NCT01083199PHASE4COMPLETEDGlobal Performance Evaluation of the AMS CONTINUUM™ Device
NCT01136226PHASE4COMPLETEDEvaluate Recovery of Testosterone for Patients Using Eligard
NCT01161563PHASE4COMPLETEDRandomized Crossover Trial to Assess the Tolerability of Gonadotropin Releasing Hormone (GnRH) Analogue Administration
NCT01230905PHASE4COMPLETEDStudy to Monitor the Effects of Androgen Suppression Treatment on the Heart
NCT01296672PHASE4COMPLETED3 Month Finasteride Challenge Test Can Significantly Improve the Performance of Screening for Prostate Cancer
NCT01365143PHASE4TERMINATEDProspective Randomized Trial Comparing Robotic Versus Open Radical Prostatectomy
NCT01379742PHASE4UNKNOWNComparison of Between ThinSeed™ and OncoSeed™ for Permanent Prostate Brachytherapy
NCT01486563PHASE4COMPLETEDHydroxyethyl Starch and Renal Function After Radical Prostatectomy
NCT01511874PHASE4COMPLETEDEfficacy and Safety Study of ELIGARD 22.5mg With Prostate Cancer
NCT01512472PHASE4TERMINATEDFirmagon (Degarelix) Intermittent Therapy
NCT01547416PHASE4COMPLETEDThe Effect of Combined General/Epidural Anesthesia Versus General Anesthesia on Diaphragmatic Function
NCT01571544PHASE4COMPLETEDThe Use of Thermal Suits as Preventing Hypothermia During Surgery
NCT01581749PHASE4UNKNOWNEvaluation of Truebeam for Low-Intermediate Risk Prostate Cancer
NCT01649635PHASE4COMPLETEDStudy of Cabazitaxel Combined With Prednisone and Prophylaxis of Neutropenia Complications in the Treatment of Patients With Metastatic Castration-resistant Prostate Cancer

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.