POP4

gene
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Also known as RPP29

Summary

POP4 (POP4 ribonuclease P/MRP subunit, HGNC:30081) is a protein-coding gene on chromosome 19q12, encoding Ribonuclease P protein subunit p29 (O95707). Component of ribonuclease P, a ribonucleoprotein complex that generates mature tRNA molecules by cleaving their 5’-ends. It is a selective cancer dependency (DepMap: 86.8% of cell lines).

This gene encodes one of the protein subunits of the small nucleolar ribonucleoprotein complexes: the endoribonuclease for mitochondrial RNA processing complex and the ribonuclease P complex. The encoded protein is localized to the nucleus and associates directly with the RNA component of these complexes. This protein is involved in processing of precursor RNAs. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 10775 — RefSeq curated summary.

At a glance

  • GWAS associations: 7
  • Clinical variants (ClinVar): 62 total
  • Cancer dependency (DepMap): dependent in 86.8% of screened cell lines
  • MANE Select transcript: NM_006627

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:30081
Approved symbolPOP4
NamePOP4 ribonuclease P/MRP subunit
Location19q12
Locus typegene with protein product
StatusApproved
AliasesRPP29
Ensembl geneENSG00000105171
Ensembl biotypeprotein_coding
OMIM606114
Entrez10775

Gene structure

Transcript identifiers

Ensembl transcripts: 15 — 6 protein_coding, 4 retained_intron, 3 protein_coding_CDS_not_defined, 2 nonsense_mediated_decay

ENST00000221770, ENST00000585603, ENST00000586136, ENST00000586173, ENST00000586420, ENST00000586823, ENST00000587232, ENST00000588551, ENST00000590688, ENST00000591061, ENST00000591824, ENST00000592749, ENST00000592759, ENST00000858464, ENST00000912733

RefSeq mRNA: 1 — MANE Select: NM_006627 NM_006627

CCDS: CCDS12416

Canonical transcript exons

ENST00000585603 — 7 exons

ExonStartEnd
ENSE000008215732961524429617237
ENSE000035375752961387129613972
ENSE000035829692961040929610632
ENSE000036231332960865729608709
ENSE000036522512961186229611939
ENSE000036914062961211729612178
ENSE000036944982960628329606325

Expression profiles

Bgee: expression breadth ubiquitous, 296 present calls, max score 95.86.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 26.1599 / max 162.5754, expressed in 1823 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
17500426.11581823
1750050.044221

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
right adrenal glandUBERON:000123395.86gold quality
right adrenal gland cortexUBERON:003582795.67gold quality
left adrenal glandUBERON:000123495.31gold quality
granulocyteCL:000009495.19gold quality
right coronary arteryUBERON:000162595.14gold quality
left adrenal gland cortexUBERON:003582595.06gold quality
mucosa of transverse colonUBERON:000499195.00gold quality
buccal mucosa cellCL:000233694.99gold quality
left coronary arteryUBERON:000162694.91gold quality
lower esophagus muscularis layerUBERON:003583394.88gold quality
lower esophagusUBERON:001347394.87gold quality
olfactory segment of nasal mucosaUBERON:000538694.82gold quality
descending thoracic aortaUBERON:000234594.70gold quality
body of pancreasUBERON:000115094.52gold quality
adrenal cortexUBERON:000123594.47gold quality
esophagusUBERON:000104394.41gold quality
rectumUBERON:000105294.37gold quality
popliteal arteryUBERON:000225094.35gold quality
tibial arteryUBERON:000761094.35gold quality
transverse colonUBERON:000115794.30gold quality
body of stomachUBERON:000116194.30gold quality
esophagogastric junction muscularis propriaUBERON:003584194.30gold quality
coronary arteryUBERON:000162194.27gold quality
aortaUBERON:000094794.19gold quality
esophagus mucosaUBERON:000246994.16gold quality
adrenal glandUBERON:000236994.13gold quality
thoracic aortaUBERON:000151594.11gold quality
apex of heartUBERON:000209894.11gold quality
calcaneal tendonUBERON:000370194.08gold quality
islet of LangerhansUBERON:000000694.07gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes8.23
E-CURD-11no217.44

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

52 targeting POP4, 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-6833-3P100.0070.633197
HSA-MIR-6851-5P100.0065.631294
HSA-MIR-3689D100.0066.141181
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-311999.9271.342390
HSA-MIR-612499.8769.783551
HSA-MIR-30A-3P99.8769.742928
HSA-MIR-30D-3P99.8769.922917
HSA-MIR-30E-3P99.8769.682942
HSA-MIR-442099.8270.081624
HSA-MIR-6515-3P99.8268.191933
HSA-MIR-181B-2-3P99.8170.061646
HSA-MIR-181B-3P99.8170.061646
HSA-MIR-4694-3P99.7969.532640
HSA-MIR-129999.7771.242389
HSA-MIR-5002-5P99.7670.841763
HSA-MIR-674599.7465.331321
HSA-MIR-1212999.7267.451311
HSA-MIR-4802-3P99.7270.131273
HSA-MIR-431099.5968.842527
HSA-MIR-6727-3P99.4965.921333
HSA-MIR-127599.4767.902749
HSA-MIR-363-5P99.4664.511015
HSA-MIR-377-3P99.3770.181905
HSA-MIR-4722-3P99.3565.221099
HSA-MIR-145-3P99.3367.66764
HSA-MIR-450599.2767.812678

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 86.8% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 4)

  • Rpp29 represses H3.3 nucleosome deposition, a finding with implications for epigenetic regulation. (PMID:26842893)
  • Collectively, the present results suggest that PhoRpp21 binds the loop between P11 and P12 helices through overall positively charged clusters on the surface of the complex and serves as a scaffold for PhoRpp29 to optimize structural conformation of its N-terminal helix (alpha2) in PhoRpp21, as well as C-terminal residues in PhoRpp29, for RNase P activity. (PMID:27810361)
  • Results demonstrate that Rpp29 promotes homology-directed repair of double-strand breaks. It is rapidly and transiently recruited to laser-microirradiated DNA sites. (PMID:28432356)
  • Rpp29 regulates H3.3-mediated epigenetic mechanisms by processing a transcribed signal that recruits H3.3 to its incorporation sites (PMID:29921582)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriopop4ENSDARG00000101472
mus_musculusPop4ENSMUSG00000030423
rattus_norvegicusPop4ENSRNOG00000027646
drosophila_melanogasterPop4FBGN0035831
caenorhabditis_eleganspopl-4WBGENE00007603

Protein

Protein identifiers

Ribonuclease P protein subunit p29O95707 (reviewed: O95707)

All UniProt accessions (6): A0A0A0MQS4, O95707, K7EK50, K7EQV2, K7ERD7, K7ESH8

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. 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.

Subcellular location. Nucleus. Nucleolus.

Similarity. Belongs to the eukaryotic/archaeal RNase P protein component 1 family.

RefSeq proteins (1): NP_006618* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR002730Rpp29/RNP1Family
IPR016848RNase_P/MRP_Rpp29-subunitFamily
IPR023534Rof/RNase_P-likeHomologous_superfamily
IPR036980RNase_P/MRP_Rpp29_sfHomologous_superfamily

Pfam: PF01868

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 (3 total): chain 1, modified residue 1, sequence conflict 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-O95707-F183.970.42

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 (1): 10

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

IDPathway
R-HSA-6784531tRNA processing in the nucleus
R-HSA-72306tRNA processing
R-HSA-8953854Metabolism of RNA

MSigDB gene sets: 171 (showing top): GOBP_RIBOSOME_BIOGENESIS, GOMF_ENDONUCLEASE_ACTIVITY, GOMF_RNA_NUCLEASE_ACTIVITY, MORF_MSH3, GOMF_NUCLEASE_ACTIVITY, SHEPARD_CRASH_AND_BURN_MUTANT_UP, MORF_BRCA1, GOBP_TRNA_METABOLIC_PROCESS, MORF_ATRX, PUJANA_CHEK2_PCC_NETWORK, WEI_MYCN_TARGETS_WITH_E_BOX, GOMF_RNA_ENDONUCLEASE_ACTIVITY, KOYAMA_SEMA3B_TARGETS_UP, MORF_PPP5C, MORF_RAP1A

GO Biological Process (4): tRNA 5’-leader removal (GO:0001682), rRNA processing (GO:0006364), RNA processing (GO:0006396), 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 (6): ribonuclease MRP complex (GO:0000172), nucleoplasm (GO:0005654), nucleolus (GO:0005730), ribonuclease P complex (GO:0030677), multimeric ribonuclease P complex (GO:0030681), nucleus (GO:0005634)

Reactome top-level categories

Rollup of top-2 pathways:

CategoryPathways
tRNA processing1
Metabolism of RNA1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
RNA processing2
endoribonuclease complex2
nuclear lumen2
tRNA 5’-end processing1
rRNA metabolic process1
ribosome biogenesis1
gene expression1
RNA biosynthetic process1
primary metabolic process1
tRNA metabolic process1
RNA binding1
nucleic acid binding1
tRNA-specific ribonuclease activity1
RNA endonuclease activity producing 5’-phosphomonoesters, hydrolytic mechanism1
binding1
sno(s)RNA-containing ribonucleoprotein complex1
cellular anatomical structure1
intracellular membraneless organelle1
ribonucleoprotein complex1
ribonuclease P complex1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

1386 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
POP4RPP30P78346999
POP4RPP38P78345998
POP4RPP25Q9BUL9995
POP4RPP40O75818994
POP4POP5Q969H6993
POP4POP7O75817769
POP4POP1Q99575667
POP4FBLP22087578
POP4RPP21Q9H633543
POP4DCLRE1AQ6PJP8519
POP4PRORPO15091453
POP4RPL23AP29316431
POP4ADI1Q9BV57430
POP4RPP25LQ8N5L8415
POP4LINC03042Q6ZUL3359

IntAct

86 interactions, top by confidence:

ABTypeScore
POP1POP4psi-mi:“MI:0915”(physical association)0.740
RPP38POP4psi-mi:“MI:0915”(physical association)0.740
POP4RPP38psi-mi:“MI:0915”(physical association)0.740
POP4RPP14psi-mi:“MI:0915”(physical association)0.740
POP5POP4psi-mi:“MI:0915”(physical association)0.670
POP4POP5psi-mi:“MI:0915”(physical association)0.670
POP4RPP25psi-mi:“MI:0915”(physical association)0.670
RPP25POP4psi-mi:“MI:0915”(physical association)0.670
POP4POP7psi-mi:“MI:0914”(association)0.640
C18orf21POP7psi-mi:“MI:0914”(association)0.640
TOR1AIP2TMEM223psi-mi:“MI:0914”(association)0.530
VSIG4TCAF2psi-mi:“MI:0914”(association)0.530
IL13RA2METTL15psi-mi:“MI:0914”(association)0.530
IL20RAUPK3BL1psi-mi:“MI:0914”(association)0.530
RPL18ARRP8psi-mi:“MI:0914”(association)0.530
POP4NME2P1psi-mi:“MI:0914”(association)0.530
PPP1R15APOP4psi-mi:“MI:0914”(association)0.530
RPP21POP7psi-mi:“MI:0914”(association)0.530
VTNHAT1psi-mi:“MI:0914”(association)0.530
RBM4NVLpsi-mi:“MI:0914”(association)0.530
POP7RPP40psi-mi:“MI:0914”(association)0.530
POP4RPP40psi-mi:“MI:0914”(association)0.530

BioGRID (147): POP1 (Affinity Capture-MS), RPP25L (Affinity Capture-MS), C3orf17 (Affinity Capture-MS), PRKCSH (Affinity Capture-MS), NPM1 (Affinity Capture-MS), RPP40 (Affinity Capture-MS), POP5 (Affinity Capture-MS), C18orf21 (Affinity Capture-MS), RPP38 (Affinity Capture-MS), POP7 (Affinity Capture-MS), RPP14 (Affinity Capture-MS), RPP30 (Affinity Capture-MS), RPP25 (Affinity Capture-MS), POP4 (Affinity Capture-MS), POP4 (Affinity Capture-MS)

ESM2 similar proteins: A6QPQ5, A9X1A9, O95707, P0C2C1, P82664, P82670, P82675, P82915, P82919, P82933, Q08BI9, Q0P5E7, Q0VFH6, Q2KIB9, Q2KID9, Q2KIJ6, Q2TBK2, Q2TBR2, Q3MHY7, Q3SYS0, Q3T040, Q58DQ5, Q58DV5, Q5C9Z4, Q5R7B0, Q5REJ1, Q5REY4, Q5RFM3, Q641X9, Q7Z2W9, Q7Z7H8, Q8N3Z3, Q8TCC3, Q924T2, Q99N85, Q99N87, Q99N94, Q9BSH4, Q9BYD2, Q9BYD6

Diamond homologs: O28362, O95707, P38336, Q2KIB9, Q5M882, Q5R7B0, Q8U007, Q9CR08, Q9P7W9, Q9ZW76, A1RXG4, A2BMC7, A3DNB5, A5UL80, A6UQ52, A6UWU6, A8AA22, A9A5I7, B0R664, B6YSM2, B8D5W2, C6A168, O24785, O26119, O59425, P14022, P22527, P60832, P60834, Q12ZU3, Q2NFW5, Q46GA3, Q57903, Q5JDH8, Q8PV42, Q8TGY6, Q8TRT9, Q97BW8, Q9V1U4, Q9YF79

SIGNOR signaling

2 interactions.

AEffectBMechanism
POP4“form complex”“Ribonuclease MRP complex”binding
POP4“form complex”“Nucleolar ribonuclease P complex”binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 91 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 processing638.9×4e-07
tRNA processing in the nucleus932.2×4e-10
rRNA processing in the nucleus and cytosol1029.2×3e-10
rRNA processing1026.6×3e-10
Major pathway of rRNA processing in the nucleolus and cytosol1314.6×3e-10
Metabolism of RNA107.6×3e-05

GO biological processes:

GO termPartnersFoldFDR
tRNA processing557.7×4e-06
rRNA processing1121.3×9e-10
ribosomal small subunit biogenesis515.6×2e-03
cytoplasmic translation615.2×4e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance41
Likely benign4
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

0 predictions. Top by Δscore:

AlphaMissense

1444 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
19:29611893:T:AW106R0.995
19:29611893:T:CW106R0.995
19:29612166:G:CA138P0.995
19:29612164:G:AG137E0.994
19:29615306:G:TG197W0.994
19:29615307:G:AG197E0.994
19:29612151:G:CA133P0.993
19:29613879:T:CS145P0.992
19:29615254:G:CK179N0.992
19:29615254:G:TK179N0.992
19:29615337:G:CR207P0.991
19:29613910:G:AG155E0.990
19:29615268:T:CF184S0.990
19:29612150:G:CK132N0.989
19:29612150:G:TK132N0.989
19:29612152:C:AA133E0.989
19:29612163:G:TG137W0.989
19:29612158:T:CL135P0.988
19:29611915:T:CL113P0.987
19:29612167:C:AA138D0.987
19:29613880:C:TS145F0.987
19:29613925:A:TE160V0.987
19:29615356:A:CK213N0.987
19:29615356:A:TK213N0.987
19:29612164:G:TG137V0.986
19:29612143:T:CL130P0.985
19:29613871:T:AV142E0.985
19:29613909:G:AG155R0.985
19:29613909:G:CG155R0.985
19:29611891:T:CL105P0.984

dbSNP variants (sampled 300 via entrez): RS1000012428 (19:29613266 C>G,T), RS1000661202 (19:29617326 C>A), RS1000879744 (19:29606903 G>A), RS1000928579 (19:29617140 T>C), RS1001480607 (19:29609535 T>A,C), RS1001511639 (19:29609293 C>A), RS1001785488 (19:29614321 G>A,T), RS1001844033 (19:29610387 G>A,C,T), RS1001994135 (19:29612475 G>T), RS1002005480 (19:29605534 A>AT), RS1002079486 (19:29617593 T>C), RS1002386441 (19:29607252 C>T), RS1002582500 (19:29609531 G>C), RS1002659911 (19:29615016 T>C), RS1002876260 (19:29604545 C>A,T)

Disease associations

OMIM: gene MIM:606114 | 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
GCST005787_29Heart rate response to exercise3.000000e-09
GCST005845_11Heart rate increase in response to exercise1.000000e-09
GCST005848_7Heart rate response to recovery post exercise (50 sec)1.000000e-09
GCST005849_9Heart rate response to recovery post exercise (40 sec)4.000000e-09
GCST005951_21Body mass index4.000000e-09
GCST009391_657Metabolite levels2.000000e-06
GCST009391_66Metabolite levels7.000000e-06

EFO canonical traits (5, from GWAS)

EFO IDTrait name
EFO:0009184heart rate response to exercise
EFO:0009185heart rate response to recovery post exercise
EFO:0004340body mass index
EFO:0010507lactose measurement
EFO:0010352diacylglycerol 34:1 measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

20 total (human), top 20 by PubMed support.

ChemicalActions (top 5)PubMed papers
sodium arseniteaffects cotreatment, increases abundance, increases expression4
Cisplatinincreases expression, affects response to substance2
GSK-J4decreases expression1
TAK-243increases sumoylation1
bisphenol Adecreases expression1
manganese chlorideaffects cotreatment, increases abundance, increases expression1
di-n-butylphosphoric acidaffects expression1
K 7174decreases expression1
ICG 001decreases expression1
Air Pollutantsdecreases expression, increases abundance1
Arsenicaffects cotreatment, increases abundance, increases expression1
Copperaffects binding, decreases expression1
Disulfiramaffects binding, decreases expression1
Manganeseaffects cotreatment, increases abundance, increases expression1
Ribonucleotidesaffects binding1
Smokedecreases expression1
T-2 Toxinincreases expression1
Sodium Seleniteincreases expression1
Lactic Aciddecreases 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.