RPP14

gene
On this page

Also known as P14

Summary

RPP14 (ribonuclease P/MRP subunit p14, HGNC:30327) is a protein-coding gene on chromosome 3p14.3, encoding Ribonuclease P protein subunit p14 (O95059). Component of ribonuclease P, a ribonucleoprotein complex that generates mature tRNA molecules by cleaving their 5’-ends. It is a common-essential gene (DepMap: required in 96.9% of cancer cell lines).

This gene encodes a subunit of ribonuclease P and has 3’ to 5’ exoribonuclease activity. Transcripts for this gene are bicistronic and include a conserved downstream open reading frame for the hydroxyacyl-thioester dehydratase type 2 (HTD2) gene.

Source: NCBI Gene 11102 — RefSeq curated summary.

At a glance

  • GWAS associations: 7
  • Clinical variants (ClinVar): 2 total
  • Cancer dependency (DepMap): dependent in 96.9% of screened cell lines (common-essential)
  • MANE Select transcript: NM_007042

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:30327
Approved symbolRPP14
Nameribonuclease P/MRP subunit p14
Location3p14.3
Locus typegene with protein product
StatusApproved
AliasesP14
Ensembl geneENSG00000163684
Ensembl biotypeprotein_coding
OMIM606112
Entrez11102

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 3 protein_coding, 2 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000295959, ENST00000445193, ENST00000461797, ENST00000462046, ENST00000463550, ENST00000466547

RefSeq mRNA: 2 — MANE Select: NM_007042 NM_001098783, NM_007042

CCDS: CCDS2888

Canonical transcript exons

ENST00000295959 — 6 exons

ExonStartEnd
ENSE000018748735830624558306417
ENSE000019113175831744058320193
ENSE000035323045831030958310406
ENSE000035507265831691558316993
ENSE000035973155831651558316591
ENSE000036928975831050758310591

Expression profiles

Bgee: expression breadth ubiquitous, 167 present calls, max score 91.57.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.3257 / max 15.2469, expressed in 145 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
370398.05211774
370406.99401740
370410.3257145

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
hindlimb stylopod muscleUBERON:000425291.57gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099189.60gold quality
muscle of legUBERON:000138388.80gold quality
gastrocnemiusUBERON:000138888.53gold quality
skeletal muscle organUBERON:001489282.66gold quality
calcaneal tendonUBERON:000370182.56gold quality
mucosa of transverse colonUBERON:000499182.18gold quality
stromal cell of endometriumCL:000225582.12gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047381.55gold quality
colonic epitheliumUBERON:000039781.51gold quality
ventricular zoneUBERON:000305381.51gold quality
smooth muscle tissueUBERON:000113581.11gold quality
adrenal tissueUBERON:001830381.09gold quality
heart left ventricleUBERON:000208481.03gold quality
rectumUBERON:000105280.82gold quality
islet of LangerhansUBERON:000000680.28gold quality
embryoUBERON:000092280.17gold quality
ganglionic eminenceUBERON:000402380.17gold quality
right lobe of liverUBERON:000111480.10gold quality
cardiac ventricleUBERON:000208280.08gold quality
right atrium auricular regionUBERON:000663179.83gold quality
transverse colonUBERON:000115779.80gold quality
leukocyteCL:000073879.66gold quality
monocyteCL:000057679.53gold quality
right adrenal gland cortexUBERON:003582779.53gold quality
muscle layer of sigmoid colonUBERON:003580579.38gold quality
left adrenal glandUBERON:000123479.04gold quality
right adrenal glandUBERON:000123378.77gold quality
apex of heartUBERON:000209878.75gold quality
gall bladderUBERON:000211078.73gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes4.92

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

118 targeting RPP14, 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-9-5P100.0072.282361
HSA-MIR-3163100.0077.238605
HSA-MIR-150-5P99.9966.691976
HSA-MIR-4482-3P99.9872.503147
HSA-MIR-1229-3P99.9766.49906
HSA-MIR-6778-3P99.9667.292693
HSA-LET-7C-3P99.9573.422862
HSA-MIR-4778-3P99.9370.401818
HSA-MIR-6753-3P99.9366.57637
HSA-MIR-7107-3P99.9366.73627
HSA-MIR-515-5P99.9269.822343
HSA-MIR-519E-5P99.9269.622358
HSA-MIR-450B-5P99.9271.483175
HSA-MIR-205-3P99.9269.923165
HSA-MIR-130599.9171.433443
HSA-MIR-345-3P99.8970.231421
HSA-MIR-6783-3P99.8967.922059
HSA-MIR-1343-3P99.8966.781815
HSA-MIR-3065-3P99.8770.251407
HSA-MIR-76599.8468.242442
HSA-MIR-132399.8369.892471
HSA-MIR-6739-5P99.8067.872806
HSA-MIR-6842-5P99.8067.541587
HSA-MIR-7110-5P99.8067.841712
HSA-MIR-4668-5P99.7970.583782
HSA-MIR-11181-3P99.7566.382205
HSA-MIR-6733-5P99.7467.942759
HSA-MIR-548O-3P99.7469.302228
HSA-MIR-132-3P99.7370.561424

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 96.9% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 1)

  • A protein subunit of human RNase P, Rpp14, and its interacting partner, OIP2, have 3’–>5’ exoribonuclease activity. (PMID:11929972)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_reriorpp14ENSDARG00000011152
mus_musculusRpp14ENSMUSG00000023156
drosophila_melanogasterRpp14bFBGN0039744
drosophila_melanogasterRpp14aFBGN0085346

Protein

Protein identifiers

Ribonuclease P protein subunit p14O95059 (reviewed: O95059)

All UniProt accessions (1): O95059

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.

Subunit / interactions. RNase P consists of a catalytic RNA moiety and about 10 protein subunits; 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.

Subcellular location. Nucleus. Nucleolus.

Miscellaneous. This protein is produced by a bicistronic gene which also produces the HTD2 protein from an overlapping reading frame.

Similarity. Belongs to the eukaryotic/archaeal RNase P protein component 2 family.

RefSeq proteins (2): NP_001092253, NP_008973* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR002759Pop5/Rpp14/Rnp2-likeFamily
IPR038085Rnp2-like_sfHomologous_superfamily

Pfam: PF01900

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 (2 total): initiator methionine 1, chain 1

Structure

Experimental structures (PDB)

5 structures.

PDBMethodResolution (Å)
9UH7ELECTRON MICROSCOPY2.84
9UH9ELECTRON MICROSCOPY3.47
6AHUELECTRON MICROSCOPY3.66
6AHRELECTRON MICROSCOPY3.92
9UHAELECTRON MICROSCOPY3.93

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-O95059-F179.590.06

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: 195 (showing top): SHEPARD_BMYB_MORPHOLINO_UP, GOMF_ENDONUCLEASE_ACTIVITY, GOMF_RNA_NUCLEASE_ACTIVITY, BROWNE_HCMV_INFECTION_6HR_DN, GOMF_NUCLEASE_ACTIVITY, GOBP_TRNA_METABOLIC_PROCESS, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, GOMF_RNA_ENDONUCLEASE_ACTIVITY, TTGGAGA_MIR5155P_MIR519E, SANSOM_APC_TARGETS_UP, FLECHNER_BIOPSY_KIDNEY_TRANSPLANT_REJECTED_VS_OK_DN, MARTINEZ_RESPONSE_TO_TRABECTEDIN_DN, BURTON_ADIPOGENESIS_5, SPIELMAN_LYMPHOBLAST_EUROPEAN_VS_ASIAN_DN

GO Biological Process (2): tRNA 5’-leader removal (GO:0001682), tRNA processing (GO:0008033)

GO Molecular Function (4): ribonuclease P RNA binding (GO:0033204), RNA binding (GO:0003723), ribonuclease P activity (GO:0004526), protein binding (GO:0005515)

GO Cellular Component (7): nucleoplasm (GO:0005654), nucleolus (GO:0005730), multimeric ribonuclease P complex (GO:0030681), nucleus (GO:0005634), ribonuclease P complex (GO:0030677), endoribonuclease complex (GO:1902555), ribonucleoprotein complex (GO:1990904)

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
nuclear lumen2
tRNA 5’-end processing1
RNA processing1
tRNA metabolic process1
RNA binding1
nucleic acid binding1
tRNA-specific ribonuclease activity1
RNA endonuclease activity producing 5’-phosphomonoesters, hydrolytic mechanism1
binding1
cellular anatomical structure1
intracellular membraneless organelle1
ribonuclease P complex1
intracellular membrane-bounded organelle1
endoribonuclease complex1
ribonucleoprotein complex1
endonuclease complex1
protein-containing complex1

Protein interactions and networks

STRING

428 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
RPP14SOWAHAQ2M3V2530
RPP14KIAA1671Q9BY89512
RPP14ANKRD16Q6P6B7507
RPP14ZBTB34Q8NCN2480
RPP14TMEM154Q6P9G4447
RPP14RNF113AO15541400
RPP14PMM2O15305395
RPP14RPN2P04844370
RPP14POP5Q969H6353
RPP14POP1Q99575353
RPP14RPP30P78346353
RPP14RPP21Q9H633353
RPP14POP4O95707352
RPP14MIPEPQ99797349
RPP14TBX15Q96SF7347

IntAct

63 interactions, top by confidence:

ABTypeScore
RPP14RPP30psi-mi:“MI:0915”(physical association)0.890
RPP25POP7psi-mi:“MI:0914”(association)0.810
POP4RPP14psi-mi:“MI:0915”(physical association)0.740
RPP30POP7psi-mi:“MI:0914”(association)0.730
RPP14POP5psi-mi:“MI:0915”(physical association)0.670
RPP14RPP40psi-mi:“MI:0915”(physical association)0.670
RPP25RPP14psi-mi:“MI:0915”(physical association)0.670
RPP14RPP40psi-mi:“MI:0914”(association)0.670
C18orf21POP7psi-mi:“MI:0914”(association)0.640
POP4POP7psi-mi:“MI:0914”(association)0.640
NPM1MPHOSPH10psi-mi:“MI:0914”(association)0.610
ZNF277RPP14psi-mi:“MI:0915”(physical association)0.560
RPP14EXOSC8psi-mi:“MI:0915”(physical association)0.560
RPP14ACTN2psi-mi:“MI:0915”(physical association)0.560
GEMIN2RPP14psi-mi:“MI:0915”(physical association)0.560
POP4NME2P1psi-mi:“MI:0914”(association)0.530
RPP21POP7psi-mi:“MI:0914”(association)0.530
SNRPCSNRPGP15psi-mi:“MI:0914”(association)0.530
POP7RPP40psi-mi:“MI:0914”(association)0.530
RPP25LRPP40psi-mi:“MI:0914”(association)0.530
RPP14POP7psi-mi:“MI:0914”(association)0.530
RPP14RPP14psi-mi:“MI:0915”(physical association)0.400
RPP14PCNApsi-mi:“MI:0915”(physical association)0.370
RPP14A2Mpsi-mi:“MI:0915”(physical association)0.370

BioGRID (71): RPP14 (Affinity Capture-MS), RPP14 (Affinity Capture-MS), RPP14 (Affinity Capture-MS), RPP14 (Affinity Capture-MS), RPP14 (Affinity Capture-MS), RPP14 (Affinity Capture-MS), RPP14 (Affinity Capture-MS), RPP14 (Affinity Capture-MS), RPP14 (Affinity Capture-MS), RPP14 (Reconstituted Complex), RPP30 (Reconstituted Complex), RPP40 (Reconstituted Complex), RPP14 (Affinity Capture-MS), IGSF21 (Two-hybrid), RPP14 (Two-hybrid)

ESM2 similar proteins: A5PK00, A7X672, B0K012, O08848, O43929, O54956, O95059, P10155, P11497, P13984, P39656, P42694, P57060, Q0JNK5, Q13085, Q13572, Q28559, Q29381, Q2HJF1, Q2T9L9, Q2YDI2, Q3U2J5, Q3ZBL5, Q53PC7, Q5F480, Q5M939, Q5R6Z7, Q5R812, Q5R9U9, Q5RB79, Q5SWU9, Q5U3V9, Q66HY7, Q6DC64, Q6DFV5, Q6NU27, Q6NYU2, Q80YV4, Q86VN1, Q8BY71

Diamond homologs: O95059, Q5RB79, Q9CQH8

SIGNOR signaling

2 interactions.

AEffectBMechanism
RPP14“form complex”“Ribonuclease MRP complex”binding
RPP14“form complex”“Nucleolar ribonuclease P complex”binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 45 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 processing561.5×2e-06
tRNA processing in the nucleus747.5×2e-08
rRNA processing in the nucleus and cytosol633.3×2e-06
rRNA processing630.3×2e-06
Major pathway of rRNA processing in the nucleolus and cytosol714.9×1e-05
Metabolism of RNA811.5×1e-05

GO biological processes:

GO termPartnersFoldFDR
rRNA processing621.8×2e-05

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
Benign1

Top pathogenic / likely-pathogenic (0)

SpliceAI

872 predictions. Top by Δscore:

VariantEffectΔscore
3:58310496:A:AGacceptor_gain1.0000
3:58310497:C:Gacceptor_gain1.0000
3:58310502:TTTA:Tacceptor_loss1.0000
3:58310505:A:AGacceptor_gain1.0000
3:58310505:A:Tacceptor_loss1.0000
3:58310506:G:GAacceptor_gain1.0000
3:58310506:GA:Gacceptor_gain1.0000
3:58310506:GAGA:Gacceptor_gain1.0000
3:58310506:GAGAA:Gacceptor_gain1.0000
3:58310589:G:GTdonor_gain1.0000
3:58310589:G:Tdonor_gain1.0000
3:58310589:GAGG:Gdonor_loss1.0000
3:58310591:GGTA:Gdonor_loss1.0000
3:58316587:AGCAG:Adonor_loss1.0000
3:58316589:CAGGT:Cdonor_loss1.0000
3:58316590:AGG:Adonor_loss1.0000
3:58316591:GGTA:Gdonor_loss1.0000
3:58316592:GTATG:Gdonor_loss1.0000
3:58316593:T:Adonor_loss1.0000
3:58316913:A:AGacceptor_gain1.0000
3:58316913:AGT:Aacceptor_gain1.0000
3:58316914:G:GAacceptor_gain1.0000
3:58316914:GT:Gacceptor_gain1.0000
3:58316914:GTG:Gacceptor_gain1.0000
3:58310577:G:GTdonor_gain0.9900
3:58310587:GGGAG:Gdonor_gain0.9900
3:58310588:GGAG:Gdonor_gain0.9900
3:58310588:GGAGG:Gdonor_gain0.9900
3:58310589:GAG:Gdonor_gain0.9900
3:58316510:TGCA:Tacceptor_loss0.9900

AlphaMissense

791 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
3:58316570:C:AA73D0.977
3:58316934:A:CS87R0.977
3:58316936:C:AS87R0.977
3:58316936:C:GS87R0.977
3:58316983:G:CR103P0.956
3:58317443:T:CS108P0.956
3:58317478:G:CR119S0.956
3:58317478:G:TR119S0.956
3:58316986:T:AV104E0.955
3:58310552:A:CK41N0.952
3:58310552:A:TK41N0.952
3:58316569:G:CA73P0.952
3:58317473:A:CS118R0.952
3:58317475:T:AS118R0.952
3:58317475:T:GS118R0.952
3:58316576:T:CL75S0.951
3:58310557:T:CL43P0.943
3:58316980:T:CF102S0.942
3:58317453:T:AL111H0.938
3:58317477:G:TR119M0.937
3:58316580:A:CR76S0.935
3:58316580:A:TR76S0.935
3:58316947:T:CL91P0.935
3:58310400:T:AV24D0.930
3:58317462:T:CL114S0.928
3:58317477:G:CR119T0.923
3:58310390:T:GY21D0.917
3:58316973:T:CC100R0.916
3:58310406:T:CL26P0.915
3:58316976:G:CA101P0.915

dbSNP variants (sampled 300 via entrez): RS1000274592 (3:58308684 T>G), RS1000635913 (3:58312825 G>T), RS1000643635 (3:58316767 G>A,C), RS1000969611 (3:58317989 G>A,C,T), RS1000990659 (3:58318553 T>C,G), RS1001110062 (3:58311456 A>G), RS1001188625 (3:58313747 C>A), RS1001243426 (3:58307506 C>G), RS1001318525 (3:58307920 G>A), RS1001370830 (3:58308290 T>A), RS1001373520 (3:58320654 A>G), RS1001561457 (3:58311287 T>C), RS1001563995 (3:58304480 G>A), RS1001773346 (3:58309157 C>T), RS1001818262 (3:58320375 C>G)

Disease associations

OMIM: gene MIM:606112 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

7 associations (top):

StudyTraitp-value
GCST006048_48Rheumatoid arthritis (ACPA-positive)1.000000e-08
GCST006614_139Total cholesterol levels9.000000e-09
GCST008163_613Height9.000000e-06
GCST010002_426Refractive error5.000000e-14
GCST010083_211Hemoglobin levels1.000000e-12
GCST011878_5Mitochondrial heteroplasmy measurement3.000000e-14
GCST90002401_120Platelet distribution width5.000000e-09

EFO canonical traits (4, from GWAS)

EFO IDTrait name
EFO:0004574total cholesterol measurement
EFO:0004509hemoglobin measurement
EFO:0600008mitochondrial heteroplasmy measurement
EFO:0007984platelet component distribution width

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

24 total (human), top 24 by PubMed support.

ChemicalActions (top 5)PubMed papers
Cadmium Chloridedecreases expression, increases abundance, increases expression2
aristolochic acid Iincreases expression1
dicrotophosdecreases expression1
alpha phellandrenedecreases expression1
glycidyl methacrylatedecreases expression1
sodium arseniteincreases expression, increases abundance1
di-n-butylphosphoric acidaffects expression1
2-palmitoylglycerolincreases expression1
Resveratrolaffects cotreatment, increases expression1
Air Pollutantsaffects expression, increases abundance1
Arsenicincreases abundance, increases expression1
Vehicle Emissionsdecreases expression, increases abundance1
Benzo(a)pyreneaffects methylation1
Cadmiumincreases abundance, increases expression1
Enzyme Inhibitorsdecreases activity, increases O-linked glycosylation1
Ozoneaffects expression, increases abundance1
Phthalic Acidsdecreases methylation1
Plant Extractsaffects cotreatment, increases expression1
Rotenonedecreases expression1
Smokedecreases expression1
Valproic Acidaffects expression1
Cyclosporinedecreases expression1
Copper Sulfatedecreases expression1
Particulate Matterdecreases expression, increases abundance1

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.