RUNDC1

gene
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Also known as DKFZp761H0421

Summary

RUNDC1 (RUN domain containing 1, HGNC:25418) is a protein-coding gene on chromosome 17q21.31, encoding RUN domain-containing protein 1 (Q96C34). May play a role as p53/TP53 inhibitor and thus may have oncogenic activity.

This gene encodes a protein that contains a RUN (RPIP8, UNC-14 and NESCA) domain and a coiled coil domain. The encoded protein may negatively regulate p53 transcriptional activity. This gene is a potential candidate gene for predisposition to glioma in humans.

Source: NCBI Gene 146923 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 77 total
  • MANE Select transcript: NM_173079

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:25418
Approved symbolRUNDC1
NameRUN domain containing 1
Location17q21.31
Locus typegene with protein product
StatusApproved
AliasesDKFZp761H0421
Ensembl geneENSG00000198863
Ensembl biotypeprotein_coding
OMIM619250
Entrez146923

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 5 protein_coding, 1 retained_intron

ENST00000361677, ENST00000589705, ENST00000590836, ENST00000903300, ENST00000903301, ENST00000954068

RefSeq mRNA: 3 — MANE Select: NM_173079 NM_001321381, NM_001394222, NM_173079

CCDS: CCDS11448

Canonical transcript exons

ENST00000361677 — 5 exons

ExonStartEnd
ENSE000011185274298725642987414
ENSE000011185304298934142989539
ENSE000012120934299085142995142
ENSE000012121044298056542981074
ENSE000035964934299031742990436

Expression profiles

Bgee: expression breadth ubiquitous, 238 present calls, max score 92.23.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 11.4648 / max 129.1825, expressed in 1784 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
16103311.46481784

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
Brodmann (1909) area 23UBERON:001355492.23gold quality
middle temporal gyrusUBERON:000277191.06gold quality
bronchial epithelial cellCL:000232888.01gold quality
bronchusUBERON:000218587.55gold quality
epithelium of nasopharynxUBERON:000195187.36gold quality
palpebral conjunctivaUBERON:000181285.74gold quality
primary visual cortexUBERON:000243684.99gold quality
kidney epitheliumUBERON:000481984.90silver quality
islet of LangerhansUBERON:000000684.78gold quality
ileal mucosaUBERON:000033184.76gold quality
superior frontal gyrusUBERON:000266184.39gold quality
prefrontal cortexUBERON:000045183.97gold quality
right uterine tubeUBERON:000130283.49gold quality
epithelial cell of pancreasCL:000008383.39silver quality
occipital lobeUBERON:000202183.39gold quality
urethraUBERON:000005783.26gold quality
nucleus accumbensUBERON:000188282.88gold quality
frontal cortexUBERON:000187082.79gold quality
postcentral gyrusUBERON:000258182.58gold quality
upper arm skinUBERON:000426382.42gold quality
neocortexUBERON:000195082.26gold quality
parietal lobeUBERON:000187282.18gold quality
mucosa of transverse colonUBERON:000499182.06gold quality
Brodmann (1909) area 9UBERON:001354081.95gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099181.91gold quality
gastrocnemiusUBERON:000138881.78gold quality
bloodUBERON:000017881.70gold quality
putamenUBERON:000187481.69gold quality
oviduct epitheliumUBERON:000480481.68gold quality
dorsolateral prefrontal cortexUBERON:000983481.66gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes6.50

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

64 targeting RUNDC1, 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-3613-3P100.0076.367965
HSA-MIR-513A-5P100.0069.772465
HSA-MIR-4425100.0067.591049
HSA-MIR-3692-3P99.9870.272139
HSA-MIR-314899.9775.066478
HSA-MIR-6778-3P99.9667.292693
HSA-MIR-570-3P99.9672.414910
HSA-MIR-101-3P99.9475.032230
HSA-MIR-3682-5P99.9367.971163
HSA-MIR-6780A-5P99.8866.692776
HSA-MIR-1273H-5P99.7766.322471
HSA-MIR-92A-2-5P99.7567.012164
HSA-MIR-199A-3P99.7570.48929
HSA-MIR-199B-3P99.7570.48929
HSA-MIR-3129-5P99.7570.46914
HSA-MIR-30B-3P99.7065.762325
HSA-MIR-3689A-3P99.7065.732306
HSA-MIR-3689B-3P99.7065.712311
HSA-MIR-3689C99.7065.712311
HSA-MIR-6779-5P99.7065.762363
HSA-MIR-875-3P99.6369.472548
HSA-MIR-80299.6167.701254
HSA-MIR-3136-3P99.5766.59781
HSA-MIR-7155-3P99.5766.48794
HSA-MIR-4728-3P99.4768.94981
HSA-MIR-431899.3866.941505
HSA-MIR-145-3P99.3367.66764
HSA-MIR-504-3P99.3067.181745
HSA-MIR-6504-3P99.1769.312891
HSA-MIR-7151-3P99.0469.722370

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriorundc1ENSDARG00000091962
mus_musculusRundc1ENSMUSG00000035007
rattus_norvegicusRundc1ENSRNOG00000023768
drosophila_melanogasterCG3703FBGN0040348
caenorhabditis_elegansWBGENE00020572

Protein

Protein identifiers

RUN domain-containing protein 1Q96C34 (reviewed: Q96C34)

All UniProt accessions (2): Q96C34, K7EQS2

UniProt curated annotations — full annotation on UniProt →

Function. May play a role as p53/TP53 inhibitor and thus may have oncogenic activity.

Isoforms (2)

UniProt IDNamesCanonical?
Q96C34-11yes
Q96C34-22

RefSeq proteins (3): NP_001308310, NP_001381151, NP_775102* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR004012Run_domDomain
IPR037213Run_dom_sfHomologous_superfamily
IPR058732RUNDC1_MDomain

Pfam: PF02759, PF26030

UniProt features (20 total): modified residue 4, sequence variant 4, region of interest 4, compositionally biased region 3, chain 1, domain 1, splice variant 1, sequence conflict 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q96C34-F171.420.20

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): 54, 71, 75, 497

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 68 (showing top): GOBP_EMBRYO_DEVELOPMENT_ENDING_IN_BIRTH_OR_EGG_HATCHING, MYOGENIN_Q6, GCANCTGNY_MYOD_Q6, CAGCTG_AP4_Q5, MONNIER_POSTRADIATION_TUMOR_ESCAPE_UP, SRF_Q5_01, SRF_C, GOBP_IN_UTERO_EMBRYONIC_DEVELOPMENT, HIF1_Q3, GOBP_EMBRYO_DEVELOPMENT, ACEVEDO_LIVER_CANCER_UP, TGGAAA_NFAT_Q4_01, RYTGCNWTGGNR_UNKNOWN, MEF2_03, LU_EZH2_TARGETS_DN

GO Biological Process (1): in utero embryonic development (GO:0001701)

GO Molecular Function (0):

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
chordate embryonic development1

Protein interactions and networks

STRING

332 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
RUNDC1CCDC186Q7Z3E2546
RUNDC1VPS50Q96JG6541
RUNDC1EIPR1Q53HC9496
RUNDC1VPS54Q9P1Q0485
RUNDC1VPS51Q9UID3453
RUNDC1TMF1P82094451
RUNDC1PTGES3LE9PB15442
RUNDC1VPS53Q5VIR6426
RUNDC1RAB2AP08886420
RUNDC1LRRC46Q96FV0411
RUNDC1ICA1P78506406
RUNDC1CHCHD5Q9BSY4396
RUNDC1PGAP1Q75T13396
RUNDC1VPS52Q8N1B4396
RUNDC1DYMQ7RTS9394

IntAct

11 interactions, top by confidence:

ABTypeScore
ENPP6SCAMP1psi-mi:“MI:0914”(association)0.640
INSYN2ACHUKpsi-mi:“MI:0914”(association)0.530
ALOX5DDHD2psi-mi:“MI:0914”(association)0.530
TNKSRUNDC1psi-mi:“MI:0407”(direct interaction)0.440
EFNA4NBASpsi-mi:“MI:0914”(association)0.350
DUSP16MEIOCpsi-mi:“MI:0914”(association)0.350
CCDC183PCNTpsi-mi:“MI:0914”(association)0.350
KCNE3TMEM131Lpsi-mi:“MI:0914”(association)0.350
EEF1AKMT3SMCHD1psi-mi:“MI:0914”(association)0.350
NIPAL3ILVBLpsi-mi:“MI:0914”(association)0.350

BioGRID (30): RUNDC1 (Affinity Capture-MS), RUNDC1 (Affinity Capture-MS), RUNDC1 (Affinity Capture-MS), RUNDC1 (Affinity Capture-MS), RUNDC1 (Affinity Capture-MS), RUNDC1 (Affinity Capture-MS), RUNDC1 (Affinity Capture-MS), RUNDC1 (Affinity Capture-MS), RUNDC1 (Proximity Label-MS), RUNDC1 (Proximity Label-MS), RUNDC1 (Proximity Label-MS), RUNDC1 (Proximity Label-MS), RUNDC1 (Proximity Label-MS), RUNDC1 (Proximity Label-MS), RUNDC1 (Proximity Label-MS)

ESM2 similar proteins: A0JNT9, A0JPP8, A1X157, O15169, O75145, O75335, P39880, P60469, Q07DZ5, Q08CF3, Q08E13, Q09YM8, Q2M1P5, Q2QLG9, Q2VUH7, Q32PN7, Q3TMW1, Q3UHC7, Q3UIL6, Q3UIW5, Q3UJV1, Q5DU25, Q5FWS6, Q5JU85, Q5PRF9, Q5XI59, Q5ZJ07, Q674X7, Q68UI8, Q69ZS8, Q6IPM2, Q6NZT2, Q6P402, Q6P730, Q6ZP65, Q80XS6, Q80Y83, Q8JZP9, Q8K1S6, Q8R4R9

Diamond homologs: A3KGB4, A5D7F8, A6H8I2, A6QP29, B1AVH7, B1V8A0, B5DFA1, D2H0G5, E2RP94, M0R4F8, O35179, O35180, O35964, O42287, O43048, O43307, O75791, O88811, O89100, O95759, P10569, P19706, P38753, P48566, P53258, P58802, P62993, P62994, P70297, Q09830, Q0IIM8, Q0U6X7, Q12317, Q14155, Q15811, Q1E878, Q28CB1, Q28E95, Q2KI13, Q2KJA1

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance66
Likely benign3
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

676 predictions. Top by Δscore:

VariantEffectΔscore
17:42987248:T:TAacceptor_gain1.0000
17:42987254:A:AGacceptor_gain1.0000
17:42987254:AG:Aacceptor_loss1.0000
17:42987254:AGAGT:Aacceptor_gain1.0000
17:42987255:G:GCacceptor_gain1.0000
17:42987255:GA:Gacceptor_gain1.0000
17:42987255:GAGT:Gacceptor_gain1.0000
17:42987255:GAGTG:Gacceptor_gain1.0000
17:42987411:GCGG:Gdonor_gain1.0000
17:42987413:GG:Gdonor_gain1.0000
17:42987414:GG:Gdonor_gain1.0000
17:42987415:G:GGdonor_gain1.0000
17:42987416:T:Gdonor_loss1.0000
17:42989337:GTAGG:Gacceptor_loss1.0000
17:42989338:TAG:Tacceptor_loss1.0000
17:42989339:A:ATacceptor_loss1.0000
17:42989340:G:GAacceptor_loss1.0000
17:42989536:CAAG:Cdonor_loss1.0000
17:42989538:AGG:Adonor_loss1.0000
17:42989540:GTTAG:Gdonor_loss1.0000
17:42989541:T:Adonor_loss1.0000
17:42990302:A:AGacceptor_gain1.0000
17:42990303:A:Gacceptor_gain1.0000
17:42990308:T:Aacceptor_gain1.0000
17:42990313:CCAG:Cacceptor_loss1.0000
17:42990315:A:AGacceptor_gain1.0000
17:42990315:AGAT:Aacceptor_gain1.0000
17:42990316:G:GAacceptor_gain1.0000
17:42990316:GA:Gacceptor_gain1.0000
17:42990316:GAT:Gacceptor_gain1.0000

AlphaMissense

3956 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
17:42989492:T:CL270P1.000
17:42987323:T:CL189P0.999
17:42989513:T:CL277P0.999
17:42991291:T:AW473R0.999
17:42991291:T:CW473R0.999
17:42991534:T:AW554R0.999
17:42991534:T:CW554R0.999
17:42991711:T:CF613L0.999
17:42991713:T:AF613L0.999
17:42991713:T:GF613L0.999
17:42987335:T:CL193P0.998
17:42989521:T:CF280L0.998
17:42989523:T:AF280L0.998
17:42989523:T:GF280L0.998
17:42980899:T:CL108P0.997
17:42980953:T:CL126P0.997
17:42987344:T:CL196P0.997
17:42989510:A:CD276A0.997
17:42989510:A:GD276G0.997
17:42989513:T:AL277H0.997
17:42989522:T:CF280S0.997
17:42991184:T:CL437P0.997
17:42991293:G:CW473C0.997
17:42991293:G:TW473C0.997
17:42991372:T:CF500L0.997
17:42991374:C:AF500L0.997
17:42991374:C:GF500L0.997
17:42991511:T:CL546P0.997
17:42991591:A:CS573R0.997
17:42991593:C:AS573R0.997

dbSNP variants (sampled 300 via entrez): RS1000245006 (17:42983944 A>G), RS1000443307 (17:42992837 G>T), RS1000585429 (17:42985463 G>A,C), RS1000617736 (17:42988473 G>A,C), RS1000774878 (17:42988799 C>T), RS1000877143 (17:42991892 A>C,G), RS1001289871 (17:42994029 T>C), RS1001429904 (17:42994339 A>G), RS1001762427 (17:42981583 C>T), RS1002470277 (17:42980203 T>C,G), RS1002535036 (17:42989959 T>C), RS1002652749 (17:42989758 C>G), RS1002709642 (17:42985534 T>C), RS1002835438 (17:42987973 A>G), RS1002887410 (17:42987541 A>G)

Disease associations

OMIM: gene MIM:619250 | 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

0 associations (top):

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

19 total (human), top 19 by PubMed support.

ChemicalActions (top 5)PubMed papers
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamidedecreases expression1
FR900359increases phosphorylation1
potassium chromate(VI)increases expression1
beta-methylcholineaffects expression1
avobenzonedecreases expression1
di-n-butylphosphoric acidaffects expression1
torcetrapibincreases expression1
ICG 001decreases expression1
Resveratrolaffects cotreatment, increases expression1
Atrazinedecreases expression1
Benzo(a)pyreneaffects methylation1
Caffeinedecreases phosphorylation1
Doxorubicindecreases expression1
Formaldehydedecreases expression1
Plant Extractsaffects cotreatment, increases expression1
Smokedecreases expression1
Urethanedecreases expression1
Valproic Acidincreases methylation1
Aflatoxin B1increases methylation1

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.