RPP25

gene
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Also known as FLJ20374

Summary

RPP25 (ribonuclease P/MRP subunit p25, HGNC:30361) is a protein-coding gene on chromosome 15q24.2, encoding Ribonuclease P protein subunit p25 (Q9BUL9). Component of ribonuclease P, a ribonucleoprotein complex that generates mature tRNA molecules by cleaving their 5’-ends.

Enables ribonuclease P RNA binding activity. Contributes to ribonuclease P activity. Involved in tRNA 5’-leader removal. Located in centriolar satellite and nucleoplasm. Part of multimeric ribonuclease P complex and ribonuclease MRP complex. Biomarker of autistic disorder.

Source: NCBI Gene 54913 — RefSeq curated summary.

At a glance

  • GWAS associations: 3
  • Clinical variants (ClinVar): 2 total
  • MANE Select transcript: NM_017793

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:30361
Approved symbolRPP25
Nameribonuclease P/MRP subunit p25
Location15q24.2
Locus typegene with protein product
StatusApproved
AliasesFLJ20374
Ensembl geneENSG00000178718
Ensembl biotypeprotein_coding
OMIM619235
Entrez54913

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000322177

RefSeq mRNA: 1 — MANE Select: NM_017793 NM_017793

CCDS: CCDS10274

Canonical transcript exons

ENST00000322177 — 1 exons

ExonStartEnd
ENSE000012432927495441874956772

Expression profiles

Bgee: expression breadth ubiquitous, 257 present calls, max score 95.51.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 12.5035 / max 113.6586, expressed in 1583 samples.

FANTOM5 promoters (7 alternative TSS)

Promoter IDTPM avgSamples expressed
15094410.05571503
1509461.1336690
1509450.8448537
1509430.210899
1509490.127548
1509480.092929
1509470.038119

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
vena cavaUBERON:000408795.51gold quality
parotid glandUBERON:000183194.19gold quality
lateral nuclear group of thalamusUBERON:000273694.17gold quality
ponsUBERON:000098893.63gold quality
body of tongueUBERON:001187692.64gold quality
subthalamic nucleusUBERON:000190692.58gold quality
substantia nigra pars reticulataUBERON:000196692.50gold quality
lateral globus pallidusUBERON:000247692.15gold quality
cardia of stomachUBERON:000116291.76gold quality
substantia nigra pars compactaUBERON:000196591.48gold quality
ventral tegmental areaUBERON:000269191.47gold quality
pylorusUBERON:000116691.46gold quality
heart right ventricleUBERON:000208091.36gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451191.35gold quality
inferior vagus X ganglionUBERON:000536391.00gold quality
pericardiumUBERON:000240790.50gold quality
superior vestibular nucleusUBERON:000722790.19gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450289.76gold quality
pharyngeal mucosaUBERON:000035589.58gold quality
mucosa of transverse colonUBERON:000499189.54gold quality
dorsal plus ventral thalamusUBERON:000189789.28gold quality
tongueUBERON:000172389.02gold quality
saphenous veinUBERON:000731888.94gold quality
superior surface of tongueUBERON:000737187.92gold quality
dorsal root ganglionUBERON:000004487.63gold quality
nippleUBERON:000203087.14gold quality
biceps brachiiUBERON:000150787.10gold quality
renal medullaUBERON:000036286.78gold quality
trigeminal ganglionUBERON:000167586.73gold quality
medulla oblongataUBERON:000189686.71gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes3.70

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

44 targeting RPP25, 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-6798-5P100.0065.77699
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-6825-5P99.9669.813431
HSA-MIR-767-5P99.9570.85993
HSA-MIR-6845-3P99.9466.881439
HSA-MIR-218-5P99.9372.222103
HSA-MIR-444799.8567.812900
HSA-MIR-607999.8468.541170
HSA-MIR-76599.8468.242442
HSA-MIR-63699.8069.581500
HSA-MIR-6842-5P99.8067.541587
HSA-MIR-7110-5P99.8067.841712
HSA-MIR-11181-3P99.7566.382205
HSA-MIR-6892-3P99.6866.401178
HSA-MIR-613299.6065.831554
HSA-MIR-211399.5871.221521
HSA-MIR-447299.5666.081478
HSA-MIR-7844-5P99.5568.561428
HSA-MIR-7106-5P99.5367.473574
HSA-MIR-127599.4767.902749
HSA-MIR-6722-3P99.4567.621919
HSA-MIR-6828-5P99.3169.211433
HSA-MIR-1909-3P99.0366.561662
HSA-MIR-625-5P99.0268.642031
HSA-MIR-429798.7766.952013
HSA-MIR-876-3P98.7668.23945
HSA-MIR-448398.0964.121642

Literature-anchored findings (GeneRIF, showing 6)

  • analyses of interactions with deletion mutant proteins indicate that the Alba-type core domain of both Rpp20 and Rpp25 contains most of the determinants for mutual association and P3 RNA recognition. (PMID:20215441)
  • Taken together, these findings suggest a potential role for the RPP25 gene transcript in the neurobiology of developmental brain disorders. (PMID:20632321)
  • Rpp25 is a major target of autoantibodies to the Th/To autoantigen complex (PMID:23587095)
  • Study showed the crystal structure of Rpp20/Rpp25 complex, and confirmed that Rpp20 and Rpp25 exhibit similar molecular structures to one another, to their yeast homologs (Pop7 andPop6, respectively), and to archaeal Alba proteins. These proteins do not seem to undergo significant conformational change upon RNA binding, suggesting that they interact with their cognate RNAs via a pre-formed binding surface. (PMID:29625199)
  • LINC00319 promotes migration, invasion and epithelial-mesenchymal transition process in cervical cancer by regulating miR-3127-5p/RPP25 axis. (PMID:31942724)
  • Crystal structure of human RPP20-RPP25 proteins in complex with the P3 domain of lncRNA RMRP. (PMID:33571640)

Cross-species orthologs

6 orthologs

OrganismSymbolGene ID
danio_reriorpp25aENSDARG00000101536
danio_reriorpp25bENSDARG00000112256
mus_musculusRpp25ENSMUSG00000062309
rattus_norvegicusRpp25ENSRNOG00000018812
drosophila_melanogasterRpp25FBGN0033092
caenorhabditis_elegansWBGENE00014020

Paralogs (1): RPP25L (ENSG00000164967)

Protein

Protein identifiers

Ribonuclease P protein subunit p25Q9BUL9 (reviewed: Q9BUL9)

All UniProt accessions (1): Q9BUL9

UniProt curated annotations — full annotation on UniProt →

Function. Component of ribonuclease P, a ribonucleoprotein complex that generates mature tRNA molecules by cleaving their 5’-ends. Also a component of the MRP ribonuclease complex, which cleaves pre-rRNA sequences.

Subunit / interactions. Component of nuclear RNase P and RNase MRP ribonucleoproteins. RNase P consists of a catalytic RNA moiety and 10 different protein chains; POP1, POP4, POP5, POP7, RPP14, RPP21, RPP25, RPP30, RPP38 and RPP40. Within the RNase P complex, POP1, POP7 and RPP25 form the ‘finger’ subcomplex, POP5, RPP14, RPP40 and homodimeric RPP30 form the ‘palm’ subcomplex, and RPP21, POP4 and RPP38 form the ‘wrist’ subcomplex. All subunits of the RNase P complex interact with the catalytic RNA. Several subunits of RNase P are also part of the RNase MRP complex. RNase MRP consists of a catalytic RNA moiety and about 8 protein subunits; POP1, POP7, RPP25, RPP30, RPP38, RPP40 and possibly also POP4 and POP5. POP7 forms a heterodimer with RPP25 that binds to the P3 stem loop of the catalytic RNA.

Subcellular location. Nucleus. Nucleolus.

Similarity. Belongs to the histone-like Alba family.

RefSeq proteins (1): NP_060263* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR002775DNA/RNA-bd_Alba-likeDomain
IPR036882Alba-like_dom_sfHomologous_superfamily
IPR051958Alba-like_NABFamily

Pfam: PF01918

Enzyme classification (BRENDA):

  • EC 3.1.26.5 — ribonuclease P (BRENDA: 188 organisms, 407 substrates, 80 inhibitors, 54 Km, 43 kcat entries)

Substrate kinetics (BRENDA)

24 substrates with measured Km, best-characterized 15. Km ranges are aggregated across organisms/conditions.

SubstrateKm (mM)Measurements
HUMAN PRE-TRNATYR0.0001–0.00055
PRE-TRNATYR5
PRE-TRNAASP4
PTRNATYR0.0002–0.03054
TRNA PRECURSOR4
PRE-TRNA-TYR0.00012
PRE-TRNATHR(AGT)0.0035–0.052
RNASE P RIBOSWITCH A0.0064–0.00812
TRNAPHE (G+1) PRECURSOR2
TRNATYR2
PMINI3PBUG0.00131
PRE-TRNA1
PRE-TRNA SUPS1 TRNASER0.00021
PRE-TRNA-ASP0.00031
PRE-TRNA-CYS0.00061

UniProt features (18 total): strand 6, helix 3, region of interest 2, compositionally biased region 2, modified residue 2, chain 1, sequence conflict 1, turn 1

Structure

Experimental structures (PDB)

7 structures.

PDBMethodResolution (Å)
6CWXX-RAY DIFFRACTION2.25
6LT7X-RAY DIFFRACTION2.7
9UH7ELECTRON MICROSCOPY2.84
9UH9ELECTRON MICROSCOPY3.47
6AHUELECTRON MICROSCOPY3.66
6AHRELECTRON MICROSCOPY3.92
9UHAELECTRON MICROSCOPY3.93

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9BUL9-F180.460.58

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 (2): 172, 182

Function

Pathways and Gene Ontology

Reactome pathways

6 pathways

IDPathway
R-HSA-6784531tRNA processing in the nucleus
R-HSA-6791226Major pathway of rRNA processing in the nucleolus and cytosol
R-HSA-72306tRNA processing
R-HSA-72312rRNA processing
R-HSA-8868773rRNA processing in the nucleus and cytosol
R-HSA-8953854Metabolism of RNA

MSigDB gene sets: 125 (showing top): ELVIDGE_HYPOXIA_DN, GOBP_RIBOSOME_BIOGENESIS, GOMF_ENDONUCLEASE_ACTIVITY, GOMF_RNA_NUCLEASE_ACTIVITY, GOMF_NUCLEASE_ACTIVITY, PEREZ_TP63_TARGETS, GOBP_TRNA_METABOLIC_PROCESS, ADDYA_ERYTHROID_DIFFERENTIATION_BY_HEMIN, CHX10_01, KIM_RESPONSE_TO_TSA_AND_DECITABINE_UP, GOMF_RNA_ENDONUCLEASE_ACTIVITY, HAMAI_APOPTOSIS_VIA_TRAIL_DN, GOBP_RIBONUCLEOPROTEIN_COMPLEX_BIOGENESIS, HOXA4_Q2, GOBP_TRNA_PROCESSING

GO Biological Process (3): tRNA 5’-leader removal (GO:0001682), rRNA processing (GO:0006364), tRNA processing (GO:0008033)

GO Molecular Function (5): RNA binding (GO:0003723), ribonuclease P RNA binding (GO:0033204), nucleic acid binding (GO:0003676), ribonuclease P activity (GO:0004526), protein binding (GO:0005515)

GO Cellular Component (6): ribonuclease MRP complex (GO:0000172), nucleoplasm (GO:0005654), nucleolus (GO:0005730), multimeric ribonuclease P complex (GO:0030681), centriolar satellite (GO:0034451), nucleus (GO:0005634)

Reactome top-level categories

Rollup of top-4 pathways:

CategoryPathways
Metabolism of RNA2
tRNA processing1
rRNA processing in the nucleus and cytosol1
rRNA processing1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
RNA processing2
binding2
nuclear lumen2
cellular anatomical structure2
tRNA 5’-end processing1
rRNA metabolic process1
ribosome biogenesis1
tRNA metabolic process1
nucleic acid binding1
RNA binding1
tRNA-specific ribonuclease activity1
RNA endonuclease activity producing 5’-phosphomonoesters, hydrolytic mechanism1
sno(s)RNA-containing ribonucleoprotein complex1
endoribonuclease complex1
intracellular membraneless organelle1
ribonuclease P complex1
centrosome1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

628 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
RPP25RPP38P78345998
RPP25RPP30P78346998
RPP25RPP40O75818995
RPP25POP4O95707995
RPP25POP5Q969H6978
RPP25POP7O75817773
RPP25SCAMP5Q8TAC9672
RPP25POP1Q99575638
RPP25QNG1Q5T6V5493
RPP25MARVELD1Q9BSK0472
RPP25FAM50AQ14320431
RPP25FAM50BQ9Y247425
RPP25ZC3HAV1LQ96H79411
RPP25RPP21Q9H633411
RPP25RPS2P15880402

IntAct

124 interactions, top by confidence:

ABTypeScore
POP7RPP25psi-mi:“MI:0915”(physical association)0.810
RPP25POP7psi-mi:“MI:0914”(association)0.810
RPP30POP7psi-mi:“MI:0914”(association)0.730
POP1RPP25psi-mi:“MI:0915”(physical association)0.670
POP4RPP25psi-mi:“MI:0915”(physical association)0.670
RPP25POP4psi-mi:“MI:0915”(physical association)0.670
RPP25POP5psi-mi:“MI:0915”(physical association)0.670
RPP25RPP14psi-mi:“MI:0915”(physical association)0.670
C18orf21POP7psi-mi:“MI:0914”(association)0.640
POP4POP7psi-mi:“MI:0914”(association)0.640
NPM1NVLpsi-mi:“MI:0914”(association)0.610
SAT1RPP25psi-mi:“MI:0915”(physical association)0.560
RPP25psi-mi:“MI:0915”(physical association)0.560
BANPRPP25psi-mi:“MI:0915”(physical association)0.560
LDOC1RPP25psi-mi:“MI:0915”(physical association)0.560
PNMA1RPP25psi-mi:“MI:0915”(physical association)0.560
KRT15RPP25psi-mi:“MI:0915”(physical association)0.560
SF3B4RPP25psi-mi:“MI:0915”(physical association)0.560
RPP25PICK1psi-mi:“MI:0915”(physical association)0.560
RPP25BACH2psi-mi:“MI:0915”(physical association)0.560
LRRC73RPP25psi-mi:“MI:0915”(physical association)0.560
DDI1RPP25psi-mi:“MI:0915”(physical association)0.560
RBPMSRPP25psi-mi:“MI:0915”(physical association)0.560
RPP25ABI2psi-mi:“MI:0915”(physical association)0.560
ZNF438RPP25psi-mi:“MI:0915”(physical association)0.560
RPP25PDLIM7psi-mi:“MI:0915”(physical association)0.560

BioGRID (110): RPP25 (Affinity Capture-MS), RPP25 (Affinity Capture-MS), RPP25 (Affinity Capture-MS), POP1 (Affinity Capture-MS), C3orf17 (Affinity Capture-MS), RPP40 (Affinity Capture-MS), POP5 (Affinity Capture-MS), RABL2A (Affinity Capture-MS), RPP38 (Affinity Capture-MS), RPP30 (Affinity Capture-MS), USP13 (Affinity Capture-MS), RPP14 (Affinity Capture-MS), C18orf21 (Affinity Capture-MS), POP7 (Affinity Capture-MS), RPP25 (Affinity Capture-MS)

ESM2 similar proteins: A6H687, A6NKF1, D3ZBP4, D3ZU57, E2RDP2, F1MH07, P0C0K6, P0DPD7, P0DPE1, P11086, Q002B5, Q08DM2, Q28F19, Q2KIR4, Q3V3V9, Q4KM32, Q4VYA0, Q568Y2, Q58CQ5, Q5E9Y5, Q5JR98, Q5JZY3, Q5PPN2, Q5RE82, Q66H85, Q684M2, Q68FW7, Q6F5E8, Q6P9Q4, Q86TL0, Q8BMZ5, Q8BYG9, Q8CDY7, Q8N5L8, Q8N8Q3, Q8TDZ2, Q8TE68, Q8VDP3, Q8WUJ1, Q91WE3

Diamond homologs: Q2KIR4, Q5PPN2, Q8IAX8, Q8N5L8, Q91WE3, Q99JH1, Q9BUL9, Q8IDN4

SIGNOR signaling

2 interactions.

AEffectBMechanism
RPP25“form complex”“Ribonuclease MRP complex”binding
RPP25“form complex”“Nucleolar ribonuclease P complex”binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 60 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
tRNA processing651.0×2e-07
tRNA processing in the nucleus942.2×1e-10
rRNA processing in the nucleus and cytosol623.0×2e-05
rRNA processing620.9×2e-05
Metabolism of RNA98.9×2e-05
Major pathway of rRNA processing in the nucleolus and cytosol68.8×2e-03

GO biological processes:

GO termPartnersFoldFDR
rRNA processing820.2×1e-06

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance0
Likely benign0
Benign2

Top pathogenic / likely-pathogenic (0)

SpliceAI

10 predictions. Top by Δscore:

VariantEffectΔscore
15:74956661:T:Cacceptor_gain0.4600
15:74956660:CT:Cacceptor_gain0.4200
15:74956661:TT:Tacceptor_gain0.4200
15:74956659:CCT:Cacceptor_gain0.3400
15:74956661:T:TCacceptor_gain0.3300
15:74956672:A:Tacceptor_gain0.2700
15:74956162:T:TGacceptor_gain0.2600
15:74956657:CGCCT:Cacceptor_gain0.2400
15:74955401:A:Tacceptor_gain0.2200
15:74955898:C:CTacceptor_gain0.2000

AlphaMissense

1263 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
15:74956384:A:GF67S0.999
15:74956329:C:AK85N0.998
15:74956329:C:GK85N0.998
15:74956351:A:TV78D0.998
15:74956356:T:AK76N0.998
15:74956356:T:GK76N0.998
15:74956426:G:TA53D0.997
15:74956336:A:GI83T0.996
15:74956174:A:GI137T0.995
15:74956344:G:CC80W0.995
15:74956357:T:AK76I0.995
15:74956358:T:CK76E0.995
15:74956390:A:TI65N0.995
15:74956447:A:GI46T0.995
15:74956174:A:TI137N0.994
15:74956331:T:CK85E0.993
15:74956339:T:AE82V0.993
15:74956345:C:TC80Y0.993
15:74956346:A:GC80R0.993
15:74956452:G:CS44R0.993
15:74956452:G:TS44R0.993
15:74956454:T:GS44R0.993
15:74956465:A:TV40D0.993
15:74956348:G:TT79K0.992
15:74956378:C:TG69D0.992
15:74956384:A:CF67C0.992
15:74956449:C:AK45N0.992
15:74956449:C:GK45N0.992
15:74956266:C:AW106C0.991
15:74956266:C:GW106C0.991

dbSNP variants (sampled 300 via entrez): RS1000060058 (15:74954080 C>G), RS1000079190 (15:74958314 C>T), RS1000193348 (15:74958036 T>C), RS1001254326 (15:74957886 A>G), RS1001362948 (15:74955224 G>A), RS1001769015 (15:74957608 C>A,G), RS1003035925 (15:74956736 G>A), RS1003254880 (15:74955803 C>A), RS1003329260 (15:74958077 T>C), RS1003330958 (15:74956865 G>A), RS1003777126 (15:74955370 G>A), RS1003932292 (15:74954044 C>T), RS1004523768 (15:74957535 C>A,G,T), RS1005878794 (15:74957016 G>A), RS1006195929 (15:74956729 G>A,C)

Disease associations

OMIM: gene MIM:619235 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

3 associations (top):

StudyTraitp-value
GCST006166_88Diastolic blood pressure x alcohol consumption interaction (2df test)3.000000e-19
GCST006434_67Systolic blood pressure x alcohol consumption interaction (2df test)2.000000e-12
GCST011365_4Myocardial infarction4.000000e-08

EFO canonical traits (3, from GWAS)

EFO IDTrait name
EFO:0004329alcohol drinking
EFO:0006336diastolic blood pressure
EFO:0006335systolic blood pressure

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, increases expression, affects expression5
sodium arseniteaffects expression, affects methylation, increases expression3
entinostatincreases expression, affects cotreatment2
Panobinostatincreases expression, affects cotreatment2
Acetaminophendecreases expression, increases expression2
Benzo(a)pyreneincreases expression, increases methylation2
Phenylmercuric Acetateaffects cotreatment, decreases expression2
methylmercuric chloridedecreases expression1
2-methyl-4-isothiazolin-3-oneincreases expression1
afimoxifeneincreases expression, decreases reaction1
potassium chromate(VI)affects cotreatment, increases expression1
ferrous chloridedecreases expression1
epigallocatechin gallateaffects cotreatment, increases expression1
di-n-butylphosphoric acidaffects expression1
tebuconazoledecreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression, decreases expression1
ICG 001decreases expression1
abrinedecreases expression1
dorsomorphindecreases expression, affects cotreatment, increases expression1
2-(1H-indazol-4-yl)-6-(4-methanesulfonylpiperazin-1-ylmethyl)-4-morpholin-4-ylthieno(3,2-d)pyrimidinedecreases expression, increases response to substance1
jinfukangincreases 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
Temozolomidedecreases expression1
Arsenicaffects expression1
Cytarabinedecreases expression1
Diazinonincreases methylation1
Doxorubicindecreases expression1
Estradiolincreases expression1
Estrogensincreases expression, decreases reaction1
Ribonucleotidesaffects binding1

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.