POP7

gene
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Also known as RPP20RPP2

Summary

POP7 (POP7 ribonuclease P/MRP subunit, HGNC:19949) is a protein-coding gene on chromosome 7q22.1, encoding Ribonuclease P protein subunit p20 (O75817). Component of ribonuclease P, a ribonucleoprotein complex that generates mature tRNA molecules by cleaving their 5’-ends. It is a selective cancer dependency (DepMap: 77.3% of cell lines).

Enables ribonuclease P RNA binding activity. Contributes to ribonuclease P activity. Involved in tRNA 5’-leader removal. Located in nucleolus. Part of multimeric ribonuclease P complex and ribonuclease MRP complex.

Source: NCBI Gene 10248 — RefSeq curated summary.

At a glance

  • GWAS associations: 13
  • Clinical variants (ClinVar): 24 total
  • Cancer dependency (DepMap): dependent in 77.3% of screened cell lines
  • MANE Select transcript: NM_005837

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:19949
Approved symbolPOP7
NamePOP7 ribonuclease P/MRP subunit
Location7q22.1
Locus typegene with protein product
StatusApproved
AliasesRPP20, RPP2
Ensembl geneENSG00000172336
Ensembl biotypeprotein_coding
OMIM606113
Entrez10248

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 13 protein_coding

ENST00000303151, ENST00000457480, ENST00000910791, ENST00000934891, ENST00000934892, ENST00000934893, ENST00000934894, ENST00000934895, ENST00000934896, ENST00000934897, ENST00000934898, ENST00000934899, ENST00000947209

RefSeq mRNA: 1 — MANE Select: NM_005837 NM_005837

CCDS: CCDS5704

Canonical transcript exons

ENST00000303151 — 2 exons

ExonStartEnd
ENSE00001130441100706121100706304
ENSE00001144096100706821100707486

Expression profiles

Bgee: expression breadth ubiquitous, 268 present calls, max score 94.06.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 38.4912 / max 192.1535, expressed in 1811 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
8005231.11121796
800517.38011753

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
prefrontal cortexUBERON:000045194.06gold quality
gastrocnemiusUBERON:000138894.02gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099193.89gold quality
right frontal lobeUBERON:000281093.66gold quality
muscle of legUBERON:000138393.61gold quality
middle temporal gyrusUBERON:000277193.55gold quality
hindlimb stylopod muscleUBERON:000425293.31gold quality
Brodmann (1909) area 9UBERON:001354093.24gold quality
skin of legUBERON:000151193.06gold quality
right lobe of liverUBERON:000111492.99gold quality
dorsolateral prefrontal cortexUBERON:000983492.81gold quality
skin of abdomenUBERON:000141692.69gold quality
mucosa of transverse colonUBERON:000499192.66gold quality
pancreatic ductal cellCL:000207992.44gold quality
cortical plateUBERON:000534392.34gold quality
right hemisphere of cerebellumUBERON:001489092.30gold quality
apex of heartUBERON:000209892.09gold quality
cerebellar hemisphereUBERON:000224592.05gold quality
cerebellar cortexUBERON:000212991.96gold quality
cingulate cortexUBERON:000302791.96gold quality
anterior cingulate cortexUBERON:000983591.95gold quality
primary visual cortexUBERON:000243691.83gold quality
Brodmann (1909) area 23UBERON:001355491.62gold quality
zone of skinUBERON:000001491.60gold quality
neocortexUBERON:000195091.43gold quality
frontal cortexUBERON:000187091.33gold quality
muscle organUBERON:000163091.13gold quality
nucleus accumbensUBERON:000188291.06gold quality
cerebellumUBERON:000203791.00gold quality
caudate nucleusUBERON:000187390.90gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes8.65
E-GEOD-109979no113.83

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

21 targeting POP7, 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-454-3P99.9174.011925
HSA-MIR-130A-3P99.9073.311861
HSA-MIR-130B-3P99.9073.271850
HSA-MIR-301A-3P99.9073.151839
HSA-MIR-301B-3P99.9073.191836
HSA-MIR-366699.9073.241833
HSA-MIR-429599.9073.111838
HSA-MIR-4671-3P99.8872.461045
HSA-MIR-394199.8670.542735
HSA-MIR-807699.7868.521170
HSA-MIR-715099.6266.801322
HSA-MIR-129099.5969.902079
HSA-MIR-1211799.5067.57868
HSA-MIR-608099.4369.43373
HSA-MIR-942-3P98.8169.04876
HSA-MIR-7113-5P97.8867.331735
HSA-MIR-512-5P97.4766.48591
HSA-MIR-4712-5P97.2467.79775
HSA-MIR-770-5P97.2468.10758
HSA-MIR-7847-3P96.6364.58952
HSA-MIR-1211594.1966.37738

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 77.3% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 3)

  • 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)
  • 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)
  • RNA binding protein POP7 regulates ILF3 mRNA stability and expression to promote breast cancer progression. (PMID:35579257)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriopop7ENSDARG00000036394
mus_musculusPop7ENSMUSG00000029715
rattus_norvegicusPop7ENSRNOG00000025310
drosophila_melanogasterRpp20FBGN0066304
caenorhabditis_elegansWBGENE00302968

Protein

Protein identifiers

Ribonuclease P protein subunit p20O75817 (reviewed: O75817)

Alternative names: Ribonucleases P/MRP protein subunit POP7 homolog

All UniProt accessions (2): O75817, C9JYM0

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 complexes. 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. Interacts with SMN1. POP7 forms a heterodimer with RPP25 that binds to the P3 stem loop of the catalytic RNA.

Subcellular location. Nucleus. Nucleolus. Cytoplasm. Cytoplasmic granule.

Similarity. Belongs to the histone-like Alba family.

RefSeq proteins (1): NP_005828* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR014612Pop7/Rpp20Family
IPR036882Alba-like_dom_sfHomologous_superfamily

Pfam: PF12328

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 (13 total): strand 6, helix 3, chain 1, mutagenesis site 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-O75817-F183.210.53

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Mutagenesis-validated functional residues (1):

PositionPhenotype
40strongly reduced interaction with rpp25.

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-6784531tRNA processing in the nucleus

MSigDB gene sets: 164 (showing top): GOBP_RIBOSOME_BIOGENESIS, GOMF_ENDONUCLEASE_ACTIVITY, GOMF_RNA_NUCLEASE_ACTIVITY, TGCGCANK_UNKNOWN, GOMF_NUCLEASE_ACTIVITY, STARK_PREFRONTAL_CORTEX_22Q11_DELETION_DN, GOBP_TRNA_METABOLIC_PROCESS, BROWNE_HCMV_INFECTION_16HR_UP, WEI_MYCN_TARGETS_WITH_E_BOX, MUELLER_PLURINET, GOMF_RNA_ENDONUCLEASE_ACTIVITY, JAZAG_TGFB1_SIGNALING_VIA_SMAD4_UP, ZHOU_INFLAMMATORY_RESPONSE_LIVE_DN, MODULE_98, FISCHER_DREAM_TARGETS

GO Biological Process (4): tRNA 5’-leader removal (GO:0001682), rRNA processing (GO:0006364), tRNA processing (GO:0008033), RNA processing (GO:0006396)

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 (7): ribonuclease MRP complex (GO:0000172), nucleus (GO:0005634), nucleoplasm (GO:0005654), nucleolar ribonuclease P complex (GO:0005655), nucleolus (GO:0005730), cytoplasm (GO:0005737), multimeric ribonuclease P complex (GO:0030681)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
tRNA 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
gene expression1
RNA biosynthetic process1
primary 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 membrane-bounded organelle1
nucleolus1
multimeric ribonuclease P complex1
nuclear protein-containing complex1
intracellular membraneless organelle1
intracellular anatomical structure1
ribonuclease P complex1

Protein interactions and networks

STRING

608 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
POP7POP5Q969H6891
POP7RPP25Q9BUL9773
POP7POP4O95707769
POP7RPLP1P05386660
POP7RPP38P78345582
POP7RPP30P78346582
POP7PTERQ96BW5557
POP7RPP40O75818447
POP7TERTO14746434
POP7RPP25LQ8N5L8432
POP7DCLRE1AQ6PJP8431
POP7POP1Q99575430
POP7LTN1O94822406
POP7PRORPO15091394
POP7NAA40Q86UY6357

IntAct

77 interactions, top by confidence:

ABTypeScore
RPP25LPOP7psi-mi:“MI:0915”(physical association)0.870
POP7RPP25Lpsi-mi:“MI:0915”(physical association)0.870
POP7RPP25psi-mi:“MI:0915”(physical association)0.810
RPP25POP7psi-mi:“MI:0914”(association)0.810
POP7LAGE3psi-mi:“MI:0915”(physical association)0.740
KBTBD7METTL15psi-mi:“MI:0914”(association)0.730
RPP30POP7psi-mi:“MI:0914”(association)0.730
C18orf21POP7psi-mi:“MI:0914”(association)0.640
POP4POP7psi-mi:“MI:0914”(association)0.640
POP7SMN1psi-mi:“MI:0407”(direct interaction)0.570
SMN1POP7psi-mi:“MI:0915”(physical association)0.570
POP7SMN1psi-mi:“MI:0403”(colocalization)0.570
C9orf72POP7psi-mi:“MI:0915”(physical association)0.560
POP7C9orf72psi-mi:“MI:0915”(physical association)0.560
RRP8NVLpsi-mi:“MI:0914”(association)0.530
POP4NME2P1psi-mi:“MI:0914”(association)0.530
RPP21POP7psi-mi:“MI:0914”(association)0.530
KLHDC3DPYSL4psi-mi:“MI:0914”(association)0.530

BioGRID (110): RPP25L (Two-hybrid), POP7 (Affinity Capture-MS), POP7 (Affinity Capture-MS), POP7 (Affinity Capture-MS), POP7 (Affinity Capture-MS), POP7 (Affinity Capture-MS), POP7 (Affinity Capture-MS), POP7 (Affinity Capture-MS), POP7 (Affinity Capture-MS), POP7 (Affinity Capture-MS), POP7 (Affinity Capture-MS), POP7 (Affinity Capture-MS), POP7 (Affinity Capture-MS), POP7 (Affinity Capture-MS), POP7 (Affinity Capture-MS)

ESM2 similar proteins: A0JNQ6, A2RT67, A2RUS2, A6NC42, A6NGQ2, A9X185, O75031, O75817, O94955, O95267, P50747, Q06VW1, Q0II25, Q0ZFW8, Q1RMS8, Q1RMZ1, Q29108, Q2TBA3, Q3T0J1, Q3TYS2, Q4VX76, Q568D5, Q568M3, Q587J7, Q5JSQ8, Q5T9G4, Q5ZLS2, Q62522, Q69ZK0, Q6AYA6, Q6P5G6, Q7Z7H3, Q80X86, Q86WV5, Q8BXK4, Q8C0Q9, Q8CHQ0, Q8TCU6, Q8WUE5, Q91Z62

Diamond homologs: O75817, Q0II25, Q2MGL3, Q9DCH2

SIGNOR signaling

2 interactions.

AEffectBMechanism
POP7“form complex”“Ribonuclease MRP complex”binding
POP7“form complex”“Nucleolar ribonuclease P complex”binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 58 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 processing759.5×4e-09
rRNA processing in the nucleus and cytosol830.6×2e-08
tRNA processing in the nucleus628.1×3e-06
rRNA processing827.9×3e-08
Major pathway of rRNA processing in the nucleolus and cytosol1014.7×6e-08
Metabolism of RNA1110.9×1e-07

GO biological processes:

GO termPartnersFoldFDR
ribosomal small subunit biogenesis522.3×3e-04
rRNA processing822.2×5e-07

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance22
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

304 predictions. Top by Δscore:

VariantEffectΔscore
7:100706301:GAGA:Gdonor_gain1.0000
7:100706303:GA:Gdonor_gain1.0000
7:100706305:G:GGdonor_gain1.0000
7:100706815:C:CAacceptor_gain0.9900
7:100706819:AG:Aacceptor_gain0.9900
7:100706820:GG:Gacceptor_gain0.9900
7:100706302:A:Tdonor_gain0.9800
7:100706818:CAGG:Cacceptor_loss0.9800
7:100706819:A:AGacceptor_gain0.9800
7:100706819:A:Cacceptor_loss0.9800
7:100706819:AGG:Aacceptor_gain0.9800
7:100706820:G:Aacceptor_loss0.9800
7:100706820:G:GGacceptor_gain0.9800
7:100706820:GGG:Gacceptor_gain0.9800
7:100706814:AC:Aacceptor_gain0.9700
7:100706300:AGAGA:Adonor_gain0.9600
7:100706301:GAGAG:Gdonor_gain0.9600
7:100706820:GGGC:Gacceptor_gain0.9600
7:100706302:AGAG:Adonor_loss0.9500
7:100706304:AG:Adonor_loss0.9500
7:100706305:G:Tdonor_loss0.9500
7:100706306:TAA:Tdonor_loss0.9500
7:100706820:GGGCA:Gacceptor_gain0.9500
7:100706307:AA:Adonor_loss0.9400
7:100706818:CAGGG:Cacceptor_gain0.9400
7:100706302:AGA:Adonor_gain0.9300
7:100706303:GAG:Gdonor_gain0.9300
7:100706314:G:GTdonor_gain0.9000
7:100706080:G:GTdonor_gain0.8900
7:100706308:AGC:Adonor_loss0.8900

AlphaMissense

896 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
7:100706946:T:AV39D1.000
7:100707053:G:CG75R1.000
7:100707054:G:AG75D1.000
7:100707054:G:TG75V1.000
7:100707084:C:AA85E1.000
7:100707219:T:AI130N1.000
7:100706942:T:GY38D0.999
7:100706984:T:CC52R0.999
7:100706985:G:AC52Y0.999
7:100706986:C:GC52W0.999
7:100707042:T:AI71N0.999
7:100707044:C:GH72D0.999
7:100707046:C:AH72Q0.999
7:100707046:C:GH72Q0.999
7:100707047:G:CG73R0.999
7:100707048:G:AG73D0.999
7:100707053:G:AG75S0.999
7:100707053:G:TG75C0.999
7:100707054:G:CG75A0.999
7:100707060:C:AA77D0.999
7:100707071:G:CA81P0.999
7:100707072:C:AA81D0.999
7:100707075:T:AI82N0.999
7:100707087:T:CL86P0.999
7:100707093:T:CL88P0.999
7:100707129:C:AA100D0.999
7:100707135:C:TT102I0.999
7:100707137:T:CS103P0.999
7:100707141:C:TT104I0.999
7:100707203:C:AR125S0.999

dbSNP variants (sampled 300 via entrez): RS1000347074 (7:100705247 C>T), RS1001309383 (7:100707254 T>A,C), RS1002349287 (7:100707441 G>A,T), RS1003357921 (7:100705226 T>G), RS1003426310 (7:100704956 G>A), RS1004713085 (7:100705525 A>G), RS1004998680 (7:100705945 T>C,G), RS1005331682 (7:100705275 G>A), RS1006323945 (7:100706718 G>A,C), RS1006355307 (7:100706389 A>C), RS1006687815 (7:100707935 C>T), RS1006890275 (7:100704262 G>A), RS1007937432 (7:100706550 C>T), RS1008972211 (7:100705299 C>A), RS1008994357 (7:100705873 C>A,T)

Disease associations

OMIM: gene MIM:606113 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

13 associations (top):

StudyTraitp-value
GCST004601_101Red blood cell count3.000000e-38
GCST004615_50Hemoglobin concentration3.000000e-14
GCST005028_7Pursuit maintenance gain in psychotic disorders1.000000e-08
GCST007201_348Schizophrenia3.000000e-06
GCST007201_74Schizophrenia1.000000e-07
GCST007932_103Medication use (thyroid preparations)1.000000e-08
GCST010204_198Low density lipoprotein cholesterol levels2.000000e-17
GCST90002383_432Hematocrit8.000000e-10
GCST90002383_433Hematocrit3.000000e-102
GCST90002384_152Hemoglobin3.000000e-29
GCST90002384_157Hemoglobin4.000000e-09
GCST90002384_158Hemoglobin9.000000e-105
GCST90002403_585Red blood cell count9.000000e-85

EFO canonical traits (6, from GWAS)

EFO IDTrait name
EFO:0004305erythrocyte count
EFO:0004509hemoglobin measurement
EFO:0008433pursuit maintenance gain measurement
EFO:0009933Thyroid preparation use measurement
EFO:0004611low density lipoprotein cholesterol measurement
EFO:0004348hematocrit

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

23 total (human), top 23 by PubMed support.

ChemicalActions (top 5)PubMed papers
sodium arsenitedecreases expression, increases expression2
aristolochic acid Iincreases expression1
bisphenol Adecreases expression1
arseniteaffects binding, increases reaction1
cobaltous chloridedecreases expression1
di-n-butylphosphoric acidaffects expression1
K 7174decreases expression1
ICG 001affects expression1
Leflunomidedecreases expression1
Benzo(a)pyreneincreases methylation1
Copperdecreases expression1
Oxygendecreases expression1
Piroxicamdecreases expression1
Ribonucleotidesaffects binding1
Smokedecreases expression1
Tretinoindecreases expression1
Valproic Acidincreases expression1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxidedecreases expression1
Asbestos, Crocidoliteincreases expression1
Thapsigargindecreases expression1
Okadaic Acidincreases expression1
Copper Sulfatedecreases expression1
Vitamin K 3affects expression1

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.