RPF2

gene
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Also known as FLJ21087bA397G5.4

Summary

RPF2 (ribosome production factor 2 homolog, HGNC:20870) is a protein-coding gene on chromosome 6q21, encoding Ribosome production factor 2 homolog (Q9H7B2). Involved in ribosomal large subunit assembly. It is a common-essential gene (DepMap: required in 98.1% of cancer cell lines).

Enables 5S rRNA binding activity. Involved in protein localization to nucleolus; regulation of signal transduction by p53 class mediator; and ribosomal large subunit biogenesis. Located in chromosome; nucleolus; and nucleoplasm.

Source: NCBI Gene 84154 — RefSeq curated summary.

At a glance

  • GWAS associations: 8
  • Clinical variants (ClinVar): 63 total
  • Cancer dependency (DepMap): dependent in 98.1% of screened cell lines (common-essential)
  • MANE Select transcript: NM_032194

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:20870
Approved symbolRPF2
Nameribosome production factor 2 homolog
Location6q21
Locus typegene with protein product
StatusApproved
AliasesFLJ21087, bA397G5.4
Ensembl geneENSG00000197498
Ensembl biotypeprotein_coding
OMIM618471
Entrez84154

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 9 protein_coding, 2 nonsense_mediated_decay

ENST00000368864, ENST00000425871, ENST00000441448, ENST00000607388, ENST00000885102, ENST00000885103, ENST00000885104, ENST00000923612, ENST00000923613, ENST00000923614, ENST00000923615

RefSeq mRNA: 2 — MANE Select: NM_032194 NM_001289111, NM_032194

CCDS: CCDS5088

Canonical transcript exons

ENST00000441448 — 10 exons

ExonStartEnd
ENSE00001019312110989028110989065
ENSE00001841675111025403111028263
ENSE00003695201111015754111015856
ENSE00003697466110999711110999787
ENSE00003697855110997183110997264
ENSE00003698761110991747110991786
ENSE00003699829111008038111008137
ENSE00003701898110985006110985138
ENSE00003787476111024183111024327
ENSE00003848306110982038110982129

Expression profiles

Bgee: expression breadth ubiquitous, 255 present calls, max score 96.15.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 44.8421 / max 1905.7424, expressed in 1808 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
6927044.29161807
692690.5505302

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
tibialis anteriorUBERON:000138596.15silver quality
deltoidUBERON:000147695.77gold quality
left ventricle myocardiumUBERON:000656695.26gold quality
spermCL:000001994.99gold quality
cartilage tissueUBERON:000241894.95gold quality
myocardiumUBERON:000234994.48gold quality
esophagus squamous epitheliumUBERON:000692094.35gold quality
tendon of biceps brachiiUBERON:000818894.35gold quality
upper arm skinUBERON:000426393.98gold quality
cardiac muscle of right atriumUBERON:000337993.70gold quality
tendonUBERON:000004392.75gold quality
gingival epitheliumUBERON:000194992.74gold quality
quadriceps femorisUBERON:000137792.49gold quality
tibiaUBERON:000097992.44gold quality
biceps brachiiUBERON:000150792.41gold quality
endometriumUBERON:000129592.34gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451192.34gold quality
parietal pleuraUBERON:000240092.27gold quality
gingivaUBERON:000182892.26gold quality
vastus lateralisUBERON:000137992.06gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450291.66gold quality
calcaneal tendonUBERON:000370191.65gold quality
skeletal muscle tissueUBERON:000113491.47gold quality
islet of LangerhansUBERON:000000691.46gold quality
layer of synovial tissueUBERON:000761691.35gold quality
muscle tissueUBERON:000238591.30gold quality
mucosa of sigmoid colonUBERON:000499391.29gold quality
oviduct epitheliumUBERON:000480491.03gold quality
cauda epididymisUBERON:000436090.82gold quality
pancreasUBERON:000126490.79gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 3.

ExperimentMarker?Max mean expression
E-GEOD-93593yes8.93
E-CURD-112yes8.09
E-MTAB-6142no277.84
E-ANND-3no0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

103 targeting RPF2, 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-1277-5P100.0073.955056
HSA-MIR-5692B100.0071.322622
HSA-MIR-5692C100.0071.322622
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-9-5P100.0072.282361
HSA-MIR-4692100.0067.322066
HSA-MIR-340-5P100.0072.504437
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-371B-5P99.9975.344759
HSA-MIR-451499.9967.101870
HSA-MIR-196A-1-3P99.9972.152772
HSA-MIR-3617-3P99.9867.86918
HSA-MIR-477599.9875.006394
HSA-MIR-548N99.9871.944170
HSA-MIR-373-5P99.9875.364753
HSA-MIR-616-5P99.9875.584775
HSA-MIR-3065-5P99.9771.563281
HSA-MIR-548AN99.9770.912817
HSA-MIR-590-3P99.9674.346478
HSA-MIR-568899.9673.234504
HSA-MIR-495-3P99.9672.814197
HSA-MIR-545-3P99.9570.742783
HSA-MIR-6755-5P99.9565.59464
HSA-MIR-6772-5P99.9467.01577
HSA-MIR-4760-3P99.9370.502385
HSA-MIR-6768-5P99.9267.361942
HSA-MIR-6809-3P99.9171.453814
HSA-MIR-7-1-3P99.9171.534384
HSA-MIR-7-2-3P99.9171.404394

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 98.1% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 2)

  • BXDC1 and EBNA1BP2 function in a dynamic scaffold for ribosome biogenesis. (PMID:19170763)
  • Clinical significance of ribosome production factor 2 homolog in hepatocellular carcinoma. (PMID:38307254)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriorpf2ENSDARG00000043960
mus_musculusRpf2ENSMUSG00000038510
rattus_norvegicusRpf2ENSRNOG00000000587
drosophila_melanogasterNon3FBGN0038585
caenorhabditis_elegansY54E10A.10WBGENE00021830

Protein

Protein identifiers

Ribosome production factor 2 homologQ9H7B2 (reviewed: Q9H7B2)

Alternative names: Brix domain-containing protein 1, Ribosome biogenesis protein RPF2 homolog

All UniProt accessions (4): Q9H7B2, Q5VXM9, Q5VXN0, U3KQN5

UniProt curated annotations — full annotation on UniProt →

Function. Involved in ribosomal large subunit assembly. May regulate the localization of the 5S RNP/5S ribonucleoprotein particle to the nucleolus.

Subunit / interactions. Component of a hexameric 5S RNP precursor complex, composed of 5S RNA, RRS1, RPF2/BXDC1, RPL5, RPL11 and HEATR3; this complex acts as a precursor for ribosome assembly.

Subcellular location. Nucleus. Nucleolus.

Similarity. Belongs to the RPF2 family.

RefSeq proteins (2): NP_001276040, NP_115570* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR007109BrixDomain
IPR039770Rpf2Family

Pfam: PF04427

UniProt features (8 total): compositionally biased region 2, sequence variant 2, chain 1, domain 1, region of interest 1, sequence conflict 1

Structure

Experimental structures (PDB)

5 structures.

PDBMethodResolution (Å)
8RL2ELECTRON MICROSCOPY2.84
8FL0ELECTRON MICROSCOPY2.91
9QIWELECTRON MICROSCOPY3.04
8IR1ELECTRON MICROSCOPY3.3
8IR3ELECTRON MICROSCOPY3.5

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9H7B2-F190.670.76

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 140 (showing top): GOBP_RIBOSOME_BIOGENESIS, RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP, SHEPARD_CRASH_AND_BURN_MUTANT_UP, GOBP_RIBOSOME_ASSEMBLY, GOBP_RIBOSOMAL_LARGE_SUBUNIT_ASSEMBLY, MILI_PSEUDOPODIA_HAPTOTAXIS_UP, GOBP_MATURATION_OF_LSU_RRNA, GOBP_PROTEIN_RNA_COMPLEX_ORGANIZATION, GOBP_ORGANELLE_ASSEMBLY, GOBP_SIGNAL_TRANSDUCTION_BY_P53_CLASS_MEDIATOR, GOBP_PROTEIN_LOCALIZATION_TO_ORGANELLE, GOBP_REGULATION_OF_SIGNAL_TRANSDUCTION_BY_P53_CLASS_MEDIATOR, GRYDER_PAX3FOXO1_ENHANCERS_IN_TADS, GOBP_RIBONUCLEOPROTEIN_COMPLEX_BIOGENESIS, GOBP_RIBOSOMAL_LARGE_SUBUNIT_BIOGENESIS

GO Biological Process (8): ribosomal large subunit assembly (GO:0000027), maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000463), ribosomal large subunit biogenesis (GO:0042273), regulation of signal transduction by p53 class mediator (GO:1901796), protein localization to nucleolus (GO:1902570), maturation of LSU-rRNA (GO:0000470), rRNA processing (GO:0006364), ribosome biogenesis (GO:0042254)

GO Molecular Function (4): RNA binding (GO:0003723), 5S rRNA binding (GO:0008097), rRNA binding (GO:0019843), protein binding (GO:0005515)

GO Cellular Component (4): nucleoplasm (GO:0005654), chromosome (GO:0005694), nucleolus (GO:0005730), nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
ribosomal large subunit biogenesis2
ribonucleoprotein complex biogenesis2
ribosome biogenesis2
nuclear lumen2
intracellular membraneless organelle2
protein-RNA complex assembly1
ribosome assembly1
maturation of LSU-rRNA1
signal transduction by p53 class mediator1
regulation of intracellular signal transduction1
protein localization to nucleus1
rRNA processing1
RNA processing1
rRNA metabolic process1
nucleic acid binding1
rRNA binding1
RNA binding1
binding1
cellular anatomical structure1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

3150 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
RPF2RRS1Q15050984
RPF2RPL11P25121920
RPF2NSA2O95478900
RPF2GNL2Q13823899
RPF2RPL5P46777884
RPF2EBNA1BP2Q99848867
RPF2MRTO4Q9UKD2827
RPF2GTPBP4Q9BZE4824
RPF2RSL24D1Q9UHA3810
RPF2NIP7Q9Y221794
RPF2WDR12Q9GZL7772
RPF2MDN1Q9NU22766
RPF2PAK1IP1Q9NWT1740
RPF2NMD3Q96D46725
RPF2PDCD11Q14690718

IntAct

206 interactions, top by confidence:

ABTypeScore
SART3PRPF4psi-mi:“MI:0914”(association)0.730
CFTRESYT2psi-mi:“MI:2364”(proximity)0.710
RPF2RRS1psi-mi:“MI:0915”(physical association)0.670
RPL14RRP8psi-mi:“MI:0914”(association)0.640
H1-1RRP8psi-mi:“MI:0914”(association)0.640
NOP53RRP8psi-mi:“MI:0914”(association)0.640
LIN28AIGF2BP3psi-mi:“MI:0914”(association)0.640
MECP2KPNA3psi-mi:“MI:0914”(association)0.640
RBM34RRP8psi-mi:“MI:0914”(association)0.640
NPM1MPHOSPH10psi-mi:“MI:0914”(association)0.610
DLG2RPF2psi-mi:“MI:0915”(physical association)0.560
RPL28MAGEB2psi-mi:“MI:0914”(association)0.560
NSA2TYW5psi-mi:“MI:0914”(association)0.530
MECP2GTPBP10psi-mi:“MI:0914”(association)0.530
H1-6ZNF724psi-mi:“MI:0914”(association)0.530
RBM34NVLpsi-mi:“MI:0914”(association)0.530
RRP8NVLpsi-mi:“MI:0914”(association)0.530
RPL37AMPHOSPH10psi-mi:“MI:0914”(association)0.530
ZNF2MPHOSPH10psi-mi:“MI:0914”(association)0.530
RPL18NOP56psi-mi:“MI:0914”(association)0.530
MACROH2A2PPM1Gpsi-mi:“MI:0914”(association)0.530
PRR11NVLpsi-mi:“MI:0914”(association)0.530
MAK16NVLpsi-mi:“MI:0914”(association)0.530
KNOP1DHX15psi-mi:“MI:0914”(association)0.530
RPL30RRP8psi-mi:“MI:0914”(association)0.530
ZBTB48ZBTB24psi-mi:“MI:0914”(association)0.530
PDGFBDKC1psi-mi:“MI:0914”(association)0.530

BioGRID (304): RPF2 (Affinity Capture-RNA), RPF2 (Affinity Capture-MS), RPF2 (Affinity Capture-MS), RPF2 (Affinity Capture-MS), RPF2 (Affinity Capture-MS), RPF2 (Affinity Capture-MS), RPF2 (Affinity Capture-MS), RPF2 (Affinity Capture-MS), RPF2 (Affinity Capture-MS), RPF2 (Affinity Capture-MS), RPF2 (Affinity Capture-MS), RPF2 (Affinity Capture-MS), RPF2 (Affinity Capture-MS), RPF2 (Affinity Capture-MS), KIAA0020 (Co-fractionation)

ESM2 similar proteins: A0A5F9D2E6, A1XQU3, O13784, O42387, O43395, O59865, P02377, P12001, P16149, P21533, P35980, P47911, P62847, P62848, P62849, P62850, P69090, P69091, P82915, Q2HJ41, Q2KIA6, Q2YDN6, Q2YGT9, Q3T0U2, Q4R5H5, Q56JU9, Q58DQ3, Q5E973, Q5EAV6, Q5R5F1, Q5RAQ8, Q5REY4, Q5XGS8, Q5ZJ85, Q6Y263, Q8LC83, Q90YQ0, Q90YU3, Q922U1, Q943Z6

Diamond homologs: G0SF80, P36160, Q2YDN6, Q54DJ0, Q9AWM9, Q9H7B2, Q9JJ80, Q9LUG5, Q9N3F0, Q9UUG1, Q9VEB3

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 187 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
Peptide chain elongation1921.1×2e-18
Viral mRNA Translation1921.1×2e-18
PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA1920.9×2e-18
Selenocysteine synthesis1920.0×4e-18
Eukaryotic Translation Termination1920.0×4e-18
Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)1919.6×4e-18
ZNF598 and the Ribosome-associated Quality Trigger (RQT) complex dissociate a ribosome stalled on a no-go mRNA1919.6×4e-18
Formation of a pool of free 40S subunits1918.7×8e-18

GO biological processes:

GO termPartnersFoldFDR
cytoplasmic translation1920.8×3e-17
ribosomal large subunit biogenesis718.4×1e-05
rRNA processing1613.4×2e-11
translation2112.8×6e-15
ribosomal small subunit biogenesis912.1×9e-06
negative regulation of translation1011.6×3e-06
negative regulation of viral genome replication511.1×4e-03
RNA processing810.4×1e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance46
Likely benign2
Benign1

Top pathogenic / likely-pathogenic (0)

SpliceAI

1719 predictions. Top by Δscore:

VariantEffectΔscore
6:110982125:GTAGT:Gdonor_gain1.0000
6:110982126:TAGT:Tdonor_gain1.0000
6:110982128:GT:Gdonor_gain1.0000
6:110982129:TGTA:Tdonor_loss1.0000
6:110982130:G:GGdonor_gain1.0000
6:110982130:GT:Gdonor_loss1.0000
6:110982131:T:Adonor_loss1.0000
6:110984999:T:TAacceptor_gain1.0000
6:110985004:A:AGacceptor_gain1.0000
6:110985005:G:GGacceptor_gain1.0000
6:110985005:GA:Gacceptor_gain1.0000
6:110985005:GAA:Gacceptor_gain1.0000
6:110985005:GAAA:Gacceptor_gain1.0000
6:110985134:ATGTG:Adonor_gain1.0000
6:110985135:TGTG:Tdonor_gain1.0000
6:110985135:TGTGG:Tdonor_loss1.0000
6:110985136:GTG:Gdonor_gain1.0000
6:110985136:GTGG:Gdonor_gain1.0000
6:110985137:TGGT:Tdonor_gain1.0000
6:110985138:GGTA:Gdonor_gain1.0000
6:110985139:G:Cdonor_loss1.0000
6:110985139:G:GGdonor_gain1.0000
6:110989066:G:GGdonor_gain1.0000
6:110991785:TGG:Tdonor_loss1.0000
6:110997262:TAGG:Tdonor_loss1.0000
6:110997264:GGTA:Gdonor_loss1.0000
6:110997265:G:Cdonor_loss1.0000
6:110997266:T:Adonor_loss1.0000
6:110999705:TTCCA:Tacceptor_loss1.0000
6:110999706:TCCA:Tacceptor_loss1.0000

AlphaMissense

2020 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
6:111024266:G:CR227T1.000
6:111024266:G:TR227M1.000
6:110991764:C:AP71H0.999
6:110997226:G:AG93D0.999
6:110997244:G:CR99P0.999
6:110997264:G:CG106R0.999
6:110999711:G:AG106D0.999
6:110999714:G:CR107P0.999
6:111015847:G:CR196P0.999
6:111024267:G:CR227S0.999
6:111024267:G:TR227S0.999
6:111025452:G:AG264E0.999
6:111025460:C:GH267D0.999
6:110985094:G:AG38R0.998
6:110985094:G:CG38R0.998
6:110985095:G:AG38E0.998
6:110991764:C:GP71R0.998
6:110997225:G:CG93R0.998
6:110997242:G:CK98N0.998
6:110997242:G:TK98N0.998
6:110997254:T:AN102K0.998
6:110997254:T:GN102K0.998
6:110997256:T:CL103P0.998
6:110999735:T:CL114P0.998
6:111024263:G:TR226M0.998
6:111024278:C:AA231E0.998
6:111025420:T:AN253K0.998
6:111025420:T:GN253K0.998
6:111025462:T:AH267Q0.998
6:111025462:T:GH267Q0.998

dbSNP variants (sampled 300 via entrez): RS1000058466 (6:111025807 C>T), RS1000212519 (6:110990898 TG>T), RS1000235831 (6:111021038 G>A), RS1000236581 (6:110980369 C>A), RS1000266863 (6:111020867 A>C,G), RS1000373976 (6:111015203 G>A), RS1000471709 (6:111020635 T>G), RS1000477761 (6:111003336 G>A,C,T), RS1000495852 (6:111013760 G>T), RS1000606033 (6:111019659 C>T), RS1000648908 (6:110985925 G>C), RS1000669139 (6:111025282 T>C), RS1000683298 (6:110984024 G>C), RS1000745153 (6:111015450 T>C), RS1000804510 (6:110992206 C>T)

Disease associations

OMIM: gene MIM:618471 | 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
GCST006879_15Blood metabolite levels6.000000e-25
GCST006879_16Blood metabolite levels5.000000e-08
GCST006879_17Blood metabolite levels2.000000e-26
GCST006879_23Blood metabolite levels7.000000e-31
GCST006879_24Blood metabolite levels3.000000e-25
GCST006879_3Blood metabolite levels8.000000e-29
GCST006879_4Blood metabolite levels7.000000e-37
GCST009391_1985Metabolite levels5.000000e-06

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0005058tyrosine measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
bisphenol Aincreases abundance, affects expression, decreases expression, affects cotreatment3
sodium arseniteincreases abundance, increases expression, decreases expression, affects cotreatment3
bisphenol Sdecreases methylation, increases expression, affects cotreatment3
Air Pollutantsincreases expression, decreases expression, increases abundance2
Arsenicaffects cotreatment, increases abundance, increases expression2
Estradiolincreases expression, affects expression2
Tobacco Smoke Pollutionincreases expression, affects expression2
Tretinoindecreases expression2
Valproic Acidincreases expression, affects expression2
Cyclosporineincreases expression2
Aflatoxin B1affects cotreatment, decreases expression, increases expression2
Particulate Matterincreases abundance, increases expression, decreases expression2
ginger extractaffects cotreatment, affects expression, increases abundance1
triphenyl phosphateaffects expression1
deoxynivalenolincreases expression1
sodium arsenatedecreases expression1
beta-lapachonedecreases expression, increases expression1
arseniteaffects binding, increases reaction1
methylparabendecreases expression1
tris(1,3-dichloro-2-propyl)phosphateincreases expression1
manganese chlorideincreases abundance, increases expression, affects cotreatment1
4-aminophenylarsenoxideaffects binding, decreases reaction1
di-n-butylphosphoric acidaffects expression1
CGP 52608affects binding, increases reaction1
chloropicrinincreases expression1
perfluoro-n-nonanoic acidincreases expression1
bisphenol Bincreases expression1
abrineincreases expression1
(4-amino-1,4-dihydro-3-(2-pyridyl)-5-thioxo-1,2,4-triazole)copper(II)increases expression1
jinfukangdecreases expression, affects cotreatment1

Clinical trials (associated diseases)

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

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