ESF1

gene
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Also known as bA526K24.1

Summary

ESF1 (ESF1 nucleolar pre-rRNA processing protein, HGNC:15898) is a protein-coding gene on chromosome 20p12.1, encoding ESF1 homolog (Q9H501). May constitute a novel regulatory system for basal transcription. It is a selective cancer dependency (DepMap: 88.9% of cell lines).

Enables RNA binding activity. Predicted to be involved in rRNA processing. Located in extracellular space.

Source: NCBI Gene 51575 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 138 total
  • Cancer dependency (DepMap): dependent in 88.9% of screened cell lines
  • MANE Select transcript: NM_001276380

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:15898
Approved symbolESF1
NameESF1 nucleolar pre-rRNA processing protein
Location20p12.1
Locus typegene with protein product
StatusApproved
AliasesbA526K24.1
Ensembl geneENSG00000089048
Ensembl biotypeprotein_coding
OMIM618765
Entrez51575

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 10 protein_coding

ENST00000202816, ENST00000617257, ENST00000874578, ENST00000874579, ENST00000919901, ENST00000919902, ENST00000919903, ENST00000919904, ENST00000942288, ENST00000942289

RefSeq mRNA: 2 — MANE Select: NM_001276380 NM_001276380, NM_016649

CCDS: CCDS13117

Canonical transcript exons

ENST00000617257 — 14 exons

ExonStartEnd
ENSE000006597591373372113733842
ENSE000006597601375969213759853
ENSE000006597611376677713766924
ENSE000006597621376990713770021
ENSE000006597641377133113771483
ENSE000006597651377251513772615
ENSE000006597661377515713775270
ENSE000006597671377587313776270
ENSE000008591321372837813728465
ENSE000009901271371890813718984
ENSE000009901281371736813717514
ENSE000012147621378250413783183
ENSE000039103801371432513715167
ENSE000039128211378488013784919

Expression profiles

Bgee: expression breadth ubiquitous, 282 present calls, max score 99.39.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 7.3590 / max 559.7910, expressed in 1585 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
1864706.51771552
1864680.6278253
1864690.213469

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
secondary oocyteCL:000065599.39gold quality
spermCL:000001997.70gold quality
buccal mucosa cellCL:000233696.86gold quality
cranial nerve IIUBERON:000094196.58gold quality
oocyteCL:000002396.50gold quality
tendon of biceps brachiiUBERON:000818895.44gold quality
medial globus pallidusUBERON:000247795.03gold quality
tendonUBERON:000004394.96gold quality
globus pallidusUBERON:000187594.86gold quality
calcaneal tendonUBERON:000370194.78gold quality
lateral globus pallidusUBERON:000247694.56gold quality
male germ cellCL:000001594.31gold quality
visceral pleuraUBERON:000240194.20gold quality
sural nerveUBERON:001548893.96gold quality
parietal pleuraUBERON:000240093.44gold quality
tibiaUBERON:000097993.29gold quality
pericardiumUBERON:000240793.13gold quality
inferior vagus X ganglionUBERON:000536392.85gold quality
substantia nigra pars reticulataUBERON:000196692.48gold quality
pleuraUBERON:000097792.13gold quality
subthalamic nucleusUBERON:000190691.60gold quality
blood vessel layerUBERON:000479791.54gold quality
Brodmann (1909) area 23UBERON:001355491.39gold quality
mammary ductUBERON:000176591.37gold quality
substantia nigra pars compactaUBERON:000196591.22gold quality
medulla oblongataUBERON:000189691.21gold quality
hair follicleUBERON:000207391.19gold quality
epithelium of mammary glandUBERON:000324490.96gold quality
ponsUBERON:000098890.92gold quality
corpus callosumUBERON:000233690.81gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes7.59

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

48 targeting ESF1, 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-5011-5P100.0083.465820
HSA-MIR-190A-3P100.0080.355520
HSA-MIR-3163100.0077.238605
HSA-LET-7A-3P100.0074.033932
HSA-LET-7B-3P100.0074.083913
HSA-LET-7F-1-3P100.0074.023928
HSA-MIR-98-3P100.0074.083907
HSA-MIR-1277-5P100.0073.955056
HSA-MIR-428299.9975.366408
HSA-MIR-453199.9969.703181
HSA-MIR-196A-1-3P99.9972.152772
HSA-MIR-3065-5P99.9771.563281
HSA-MIR-493-5P99.9672.472382
HSA-MIR-4666A-3P99.9671.713434
HSA-MIR-590-3P99.9674.346478
HSA-MIR-539-5P99.9370.302855
HSA-MIR-6508-5P99.9270.672465
HSA-MIR-6768-5P99.9267.361942
HSA-MIR-130599.9171.433443
HSA-MIR-652-5P99.9167.49505
HSA-MIR-3529-3P99.9073.553045
HSA-MIR-990299.8969.152250
HSA-MIR-95-5P99.8972.173973
HSA-MIR-612499.8769.783551
HSA-MIR-391999.8769.452489
HSA-MIR-806799.8669.592260
HSA-MIR-394199.8670.542735
HSA-MIR-94499.8270.853042
HSA-MIR-46699.6770.852863
HSA-MIR-1212399.5271.792990

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 88.9% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 2)

  • The Rattus rattus ABT1-associated protein formed a complex with ABT1 and suppressed activation of Pol II-directed transcription in mammalian cells. It binds and negatively regulates ABT1. (PMID:15660422)
  • Human RPF1 and ESF1 in Pre-rRNA Processing and the Assembly of Pre-Ribosomal Particles: A Functional Study. (PMID:38391939)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_rerioesf1ENSDARG00000008740
mus_musculusEsf1ENSMUSG00000045624
rattus_norvegicusEsf1ENSRNOG00000004777
drosophila_melanogasterCG11417FBGN0024364
caenorhabditis_elegansWBGENE00010231

Protein

Protein identifiers

ESF1 homologQ9H501 (reviewed: Q9H501)

Alternative names: ABT1-associated protein

All UniProt accessions (2): Q9H501, A0A087WX71

UniProt curated annotations — full annotation on UniProt →

Function. May constitute a novel regulatory system for basal transcription. Negatively regulates ABT1.

Subunit / interactions. Interacts with ABT1. Forms a complex with ABT1 and suppresses the ABT1-induced activation of polymerase II-directed transcription in mammalian cells.

Subcellular location. Nucleus. Nucleolus. Nucleoplasm.

Similarity. Belongs to the ESF1 family.

RefSeq proteins (2): NP_001263309, NP_057733 (=MANE)

Domains & families (InterPro)

IDNameType
IPR012580NUC153Domain
IPR012677Nucleotide-bd_a/b_plait_sfHomologous_superfamily
IPR039754Esf1Family
IPR056750RRM_ESF1Domain

Pfam: PF08159, PF25121

UniProt features (58 total): modified residue 22, sequence conflict 13, compositionally biased region 12, region of interest 5, sequence variant 3, initiator methionine 1, chain 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9H501-F164.810.09

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 (22): 2, 75, 77, 79, 82, 134, 153, 179, 180, 198, 296, 298, 311, 312, 313, 614, 657, 663, 693, 694 …

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 146 (showing top): TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_MONOCYTE_UP, GOBP_RIBOSOME_BIOGENESIS, RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP, WEI_MYCN_TARGETS_WITH_E_BOX, MILI_PSEUDOPODIA_HAPTOTAXIS_UP, GGCKCATGS_UNKNOWN, GOBP_RIBONUCLEOPROTEIN_COMPLEX_BIOGENESIS, BERENJENO_TRANSFORMED_BY_RHOA_UP, GOCC_NUCLEOLUS, BENPORATH_ES_1, HAMAI_APOPTOSIS_VIA_TRAIL_UP, PUIFFE_INVASION_INHIBITED_BY_ASCITES_DN, SENGUPTA_NASOPHARYNGEAL_CARCINOMA_WITH_LMP1_UP, KRIGE_RESPONSE_TO_TOSEDOSTAT_6HR_DN, FERREIRA_EWINGS_SARCOMA_UNSTABLE_VS_STABLE_UP

GO Biological Process (1): rRNA processing (GO:0006364)

GO Molecular Function (1): RNA binding (GO:0003723)

GO Cellular Component (4): obsolete extracellular space (GO:0005615), nucleoplasm (GO:0005654), nucleolus (GO:0005730), nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
nuclear lumen2
RNA processing1
rRNA metabolic process1
ribosome biogenesis1
nucleic acid binding1
cellular anatomical structure1
intracellular membraneless organelle1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

2283 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ESF1ABT1Q9ULW3876
ESF1EMG1Q92979677
ESF1DDX49Q9Y6V7660
ESF1UTP25Q68CQ4639
ESF1PDCD11Q14690634
ESF1NOP56O00567564
ESF1BYSLQ13895564
ESF1UTP20O75691555
ESF1KRI1Q8N9T8553
ESF1DDX10Q13206532
ESF1UTP4Q969X6532
ESF1HEATR1Q9H583521
ESF1DHX8Q14562475
ESF1UTP18Q9Y5J1461
ESF1SLX4IPQ5VYV7460

IntAct

115 interactions, top by confidence:

ABTypeScore
CDK8MED19psi-mi:“MI:2364”(proximity)0.850
ARL3UNC119Bpsi-mi:“MI:0914”(association)0.730
KPNA1TCERG1psi-mi:“MI:0914”(association)0.640
RBM34RRP8psi-mi:“MI:0914”(association)0.640
NPM1MPHOSPH10psi-mi:“MI:0914”(association)0.610
MECP2GTPBP10psi-mi:“MI:0914”(association)0.530
CBX6IGF2BP3psi-mi:“MI:0914”(association)0.530
ABT1ZNF316psi-mi:“MI:0914”(association)0.530
EZH1EPOPpsi-mi:“MI:0914”(association)0.530
MAGEB2GTPBP10psi-mi:“MI:0914”(association)0.530
RPLP0GTPBP10psi-mi:“MI:0914”(association)0.530
NPM1WDR46psi-mi:“MI:0914”(association)0.480
ESF1H2BC9psi-mi:“MI:0915”(physical association)0.400
ADAM19ESF1psi-mi:“MI:0915”(physical association)0.370
Srp72psi-mi:“MI:0914”(association)0.350
Faap100CDKN2Apsi-mi:“MI:0914”(association)0.350
CDK2AP1MTA3psi-mi:“MI:0914”(association)0.350
ZMYND8MTA3psi-mi:“MI:0914”(association)0.350
ITPKBPDE4Apsi-mi:“MI:0914”(association)0.350
HNRNPUpsi-mi:“MI:0914”(association)0.350
Nhsl1H3-3Bpsi-mi:“MI:0914”(association)0.350
Bcl7cSMARCD2psi-mi:“MI:0914”(association)0.350
GAR1TAF1psi-mi:“MI:0914”(association)0.350
FBXO7ELOCpsi-mi:“MI:0914”(association)0.350
RRP1BZNF785psi-mi:“MI:0914”(association)0.350
MecomESYT2psi-mi:“MI:0914”(association)0.350
ESR1ESYT2psi-mi:“MI:0914”(association)0.350

BioGRID (180): ESF1 (Affinity Capture-RNA), ESF1 (Affinity Capture-MS), AATF (Co-fractionation), DDX52 (Co-fractionation), ESF1 (Co-fractionation), ESF1 (Co-fractionation), KIAA0020 (Co-fractionation), MPHOSPH10 (Co-fractionation), SEPT7 (Co-fractionation), UTP3 (Co-fractionation), ESF1 (Affinity Capture-MS), ESF1 (Affinity Capture-MS), ESF1 (Affinity Capture-MS), ESF1 (Affinity Capture-MS), ESF1 (Affinity Capture-MS)

ESM2 similar proteins: F4JP52, F4JW79, F4K4D6, F4K4Y5, I1HNB2, O04608, O23063, O24591, O48802, O49595, P05221, P06748, P07222, P13084, P16039, P35659, P91753, Q0WNR6, Q1HTZ8, Q1HTZ9, Q1PEP5, Q3T160, Q56WH4, Q61937, Q63ZM9, Q6AXS3, Q6DJ13, Q6V9I6, Q7TNV0, Q7XTT4, Q84JB7, Q8GUP3, Q8LDF9, Q8LJS2, Q8RXT5, Q94C59, Q94IK2, Q9C8J7, Q9FVE6, Q9H501

Diamond homologs: O74828, Q06344, Q3V1V3, Q756J5, Q76MT4, Q9H501

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 152 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
Eukaryotic Translation Initiation515.0×5e-04
Cap-dependent Translation Initiation515.0×5e-04
SARS-CoV-1 modulates host translation machinery515.0×5e-04
Influenza Viral RNA Transcription and Replication714.6×4e-05
rRNA modification in the nucleus and cytosol814.5×2e-05
Influenza Infection813.7×2e-05
Nonsense-Mediated Decay (NMD)613.6×3e-04
Eukaryotic Translation Elongation513.5×6e-04

GO biological processes:

GO termPartnersFoldFDR
ribosomal small subunit biogenesis1220.6×4e-10
cytoplasmic translation912.5×2e-05
rRNA processing77.5×7e-03
translation86.2×7e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance107
Likely benign13
Benign1

Top pathogenic / likely-pathogenic (0)

SpliceAI

2275 predictions. Top by Δscore:

VariantEffectΔscore
20:13715163:TTTAC:Tacceptor_gain1.0000
20:13715164:TTAC:Tacceptor_gain1.0000
20:13715165:TAC:Tacceptor_gain1.0000
20:13715166:AC:Aacceptor_gain1.0000
20:13715167:CC:Cacceptor_gain1.0000
20:13715168:C:CCacceptor_gain1.0000
20:13715177:C:CTacceptor_gain1.0000
20:13715178:A:Tacceptor_gain1.0000
20:13717363:GTTAC:Gdonor_loss1.0000
20:13717364:TTAC:Tdonor_loss1.0000
20:13717365:TACCT:Tdonor_loss1.0000
20:13717366:A:Tdonor_loss1.0000
20:13717378:T:TAdonor_gain1.0000
20:13717387:AATT:Adonor_gain1.0000
20:13717390:T:Adonor_gain1.0000
20:13717394:T:TAdonor_gain1.0000
20:13717510:TCAGC:Tacceptor_gain1.0000
20:13717511:CAGC:Cacceptor_gain1.0000
20:13717511:CAGCC:Cacceptor_gain1.0000
20:13717512:AGC:Aacceptor_gain1.0000
20:13717512:AGCCT:Aacceptor_loss1.0000
20:13717513:GC:Gacceptor_gain1.0000
20:13717513:GCC:Gacceptor_loss1.0000
20:13717514:CCTG:Cacceptor_gain1.0000
20:13717515:C:CAacceptor_loss1.0000
20:13717515:C:CCacceptor_gain1.0000
20:13717516:T:Aacceptor_loss1.0000
20:13717517:G:Cacceptor_gain1.0000
20:13717517:G:GCacceptor_gain1.0000
20:13717525:C:CTacceptor_gain1.0000

AlphaMissense

3089 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
20:13759699:C:AW607C0.999
20:13759699:C:GW607C0.999
20:13759701:A:GW607R0.999
20:13759701:A:TW607R0.999
20:13766912:A:GW511R0.999
20:13766912:A:TW511R0.999
20:13771334:A:GL467P0.998
20:13771351:A:CS461R0.998
20:13771351:A:TS461R0.998
20:13771353:T:GS461R0.998
20:13771427:G:TA436E0.998
20:13775237:A:GW357R0.998
20:13775237:A:TW357R0.998
20:13766910:C:AW511C0.997
20:13766910:C:GW511C0.997
20:13771428:C:GA436P0.997
20:13771445:C:GR430P0.997
20:13775161:A:TV382D0.997
20:13775251:A:TV352D0.997
20:13770016:A:TI470K0.996
20:13771397:G:TA446D0.996
20:13733777:A:GW632R0.995
20:13733777:A:TW632R0.995
20:13771462:T:AR424S0.995
20:13771462:T:GR424S0.995
20:13775235:C:AW357C0.995
20:13775235:C:GW357C0.995
20:13775254:G:TA351E0.995
20:13733775:C:AW632C0.994
20:13733775:C:GW632C0.994

dbSNP variants (sampled 300 via entrez): RS1000042373 (20:13758442 A>G), RS1000076354 (20:13731475 T>C), RS1000151567 (20:13739151 A>G), RS1000158363 (20:13762082 T>A), RS1000200503 (20:13751409 G>A), RS1000207875 (20:13758282 T>C), RS1000262687 (20:13747377 G>A), RS1000284498 (20:13760181 T>A,C), RS1000302884 (20:13757917 T>A), RS1000328247 (20:13734430 A>C), RS1000403129 (20:13778641 A>G), RS1000516463 (20:13742556 C>A,T), RS1000549012 (20:13748963 T>C), RS1000620003 (20:13726570 A>G), RS1000631523 (20:13749198 T>C)

Disease associations

OMIM: gene MIM:618765 | disease phenotypes:

GenCC curated gene-disease

Mondo (1): breast ductal adenocarcinoma (MONDO:0005590)

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

MeSH disease descriptors (1)

DescriptorNameTree numbers
D018270Carcinoma, Ductal, BreastC04.557.470.200.025.232.500; C04.557.470.615.132.500; C04.588.180.390; C17.800.090.500.390

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

43 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
sodium arsenitedecreases expression, affects cotreatment, increases abundance, increases expression3
aristolochic acid Idecreases expression1
FR900359affects phosphorylation1
TAK-243increases sumoylation1
dicrotophosdecreases expression1
testosterone enanthateaffects expression1
triphenyl phosphateaffects expression1
deoxynivalenolincreases expression1
manganese chlorideincreases abundance, increases expression, affects cotreatment1
nickel sulfatedecreases expression1
coumarinincreases phosphorylation1
perfluorooctane sulfonic aciddecreases expression1
K 7174increases expression1
abrineincreases expression1
jinfukangdecreases expression1
Bortezomibincreases expression1
Resveratrolaffects cotreatment, increases expression1
Sunitinibincreases expression1
Vorinostatincreases expression1
Leflunomideincreases expression1
Air Pollutantsdecreases expression, increases abundance1
Arsenicaffects cotreatment, increases abundance, increases expression1
Benzo(a)pyreneincreases expression1
Caffeinedecreases phosphorylation1
Estradiolincreases expression1
Ethyl Methanesulfonatedecreases expression1
Formaldehydedecreases expression1
Manganeseincreases abundance, increases expression, affects cotreatment1
Phthalic Acidsdecreases methylation1
Plant Extractsaffects cotreatment, increases expression1

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT03414970PHASE3ACTIVE_NOT_RECRUITINGHypofractionated Radiation Therapy After Mastectomy in Preventing Recurrence in Patients With Stage IIa-IIIa Breast Cancer
NCT00461344PHASE2TERMINATEDDocetaxel + Doxorubicin as Neoadjuvant Chemotherapy in Patients With Breast Cancer
NCT07499999PHASE2NOT_YET_RECRUITINGRandomized Double-Blind Phase II Trial of Baby Exemestane Versus Baby Tamoxifen in Post-Menopausal Women at High Risk for Breast Cancer
NCT00637364PHASE1/PHASE2SUSPENDEDHigh Intensity Focused Ultrasound Tumor Treatment for Pancreatic Cancer Pain
NCT02779855PHASE1/PHASE2COMPLETEDTalimogene Laherparepvec in Combination With Neoadjuvant Chemotherapy in Triple Negative Breast Cancer
NCT01753908EARLY_PHASE1COMPLETEDBroccoli Sprout Extract in Treating Patients With Breast Cancer
NCT01796041EARLY_PHASE1COMPLETEDIntraoperative Imaging of Breast Cancer With Indocyanine Green
NCT01208974Not specifiedACTIVE_NOT_RECRUITINGNipple-Areola Complex (NAC) Irradiation After Nipple-Sparing Mastectomy and Reconstruction
NCT01875198Not specifiedTERMINATEDOncologic Impact of Splenectomy-omitting Radical Pancreatectomy in Well-selected Left-sided Pancreatic Cancer
NCT03543397Not specifiedUNKNOWNMRI in Ductal Carcinoma in Situ (DCIS)
NCT03834532Not specifiedCOMPLETEDLiving Well After Breast Surgery
  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): breast ductal adenocarcinoma