POP5

gene
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Summary

POP5 (POP5 ribonuclease P/MRP subunit, HGNC:17689) is a protein-coding gene on chromosome 12q24.31, encoding Ribonuclease P/MRP protein subunit POP5 (Q969H6). Component of ribonuclease P, a protein complex that generates mature tRNA molecules by cleaving their 5’-ends. It is a common-essential gene (DepMap: required in 99.1% of cancer 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 51367 — RefSeq curated summary.

At a glance

  • GWAS associations: 3
  • Clinical variants (ClinVar): 19 total — 1 pathogenic
  • Cancer dependency (DepMap): dependent in 99.1% of screened cell lines (common-essential)
  • MANE Select transcript: NM_015918

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:17689
Approved symbolPOP5
NamePOP5 ribonuclease P/MRP subunit
Location12q24.31
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000167272
Ensembl biotypeprotein_coding
OMIM609992
Entrez51367

Gene structure

Transcript identifiers

Ensembl transcripts: 22 — 15 protein_coding, 5 retained_intron, 2 protein_coding_CDS_not_defined

ENST00000341039, ENST00000357500, ENST00000511394, ENST00000535245, ENST00000539716, ENST00000541834, ENST00000542568, ENST00000542776, ENST00000543355, ENST00000906575, ENST00000906576, ENST00000906577, ENST00000906578, ENST00000906579, ENST00000906580, ENST00000906581, ENST00000906582, ENST00000930091, ENST00000930092, ENST00000930093, ENST00000930094, ENST00000930095

RefSeq mRNA: 2 — MANE Select: NM_015918 NM_015918, NM_198202

CCDS: CCDS9202, CCDS9203

Canonical transcript exons

ENST00000357500 — 5 exons

ExonStartEnd
ENSE00001379374120581115120581257
ENSE00002303901120578764120579412
ENSE00003467103120581343120581402
ENSE00003546420120579774120579923
ENSE00003667745120579514120579597

Expression profiles

Bgee: expression breadth ubiquitous, 287 present calls, max score 96.43.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 14.8707 / max 125.1835, expressed in 1785 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
13366814.87071785

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
mucosa of transverse colonUBERON:000499196.43gold quality
right adrenal glandUBERON:000123396.20gold quality
right adrenal gland cortexUBERON:003582796.09gold quality
adenohypophysisUBERON:000219695.97gold quality
metanephros cortexUBERON:001053395.67gold quality
left adrenal gland cortexUBERON:003582595.66gold quality
left adrenal glandUBERON:000123495.58gold quality
pituitary glandUBERON:000000795.53gold quality
right lobe of thyroid glandUBERON:000111995.50gold quality
adrenal cortexUBERON:000123595.32gold quality
left lobe of thyroid glandUBERON:000112094.91gold quality
right lobe of liverUBERON:000111494.90gold quality
right uterine tubeUBERON:000130294.87gold quality
spleenUBERON:000210694.71gold quality
adrenal glandUBERON:000236994.58gold quality
body of pancreasUBERON:000115094.54gold quality
thyroid glandUBERON:000204694.54gold quality
apex of heartUBERON:000209894.51gold quality
granulocyteCL:000009494.42gold quality
right atrium auricular regionUBERON:000663193.67gold quality
rectumUBERON:000105293.61gold quality
small intestine Peyer’s patchUBERON:000345493.54gold quality
left coronary arteryUBERON:000162693.49gold quality
transverse colonUBERON:000115793.42gold quality
cardiac atriumUBERON:000208193.38gold quality
right ovaryUBERON:000211893.25gold quality
adult mammalian kidneyUBERON:000008293.23gold quality
heart left ventricleUBERON:000208493.23gold quality
lymph nodeUBERON:000002993.21gold quality
ileal mucosaUBERON:000033193.18gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes10.82

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

21 targeting POP5, 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-361899.6968.571012
HSA-MIR-6716-5P99.5668.621244
HSA-MIR-7159-5P99.5372.122472
HSA-MIR-136-5P99.5067.261153
HSA-MIR-431899.3866.941505
HSA-MIR-1912-3P99.3267.40936
HSA-MIR-3692-5P99.2967.041421
HSA-MIR-1295B-5P99.0367.50810
HSA-MIR-412-3P98.8666.89712
HSA-MIR-6754-3P98.8466.60889
HSA-MIR-26B-3P98.7167.491102
HSA-MIR-4703-5P98.5370.131645
HSA-MIR-3942-5P98.5269.511517
HSA-MIR-7114-5P98.5167.871349
HSA-MIR-4662A-5P98.4867.181007
HSA-MIR-4733-3P98.3565.20994
HSA-MIR-7113-5P97.8867.331735
HSA-MIR-3190-3P97.6166.951406
HSA-MIR-428897.1167.231636
HSA-MIR-6858-3P96.3764.41771
HSA-MIR-286195.2465.471056

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 99.1% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 2)

  • Molecular mechanism by which Cartilage-hair hypolasia-associated mutations affect the function of RNase MRP. (PMID:18164267)
  • archaeal homologs of the human RNase P proteins Pop5 and Rpp30 (PMID:25704799)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriopop5ENSDARG00000053452
mus_musculusPop5ENSMUSG00000060152
rattus_norvegicusPop5ENSRNOG00000001199
drosophila_melanogasterPop5FBGN0036696
caenorhabditis_elegansWBGENE00013422

Protein

Protein identifiers

Ribonuclease P/MRP protein subunit POP5Q969H6 (reviewed: Q969H6)

All UniProt accessions (1): Q969H6

UniProt curated annotations — full annotation on UniProt →

Function. Component of ribonuclease P, a protein 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.

Subcellular location. Nucleus. Nucleolus.

Miscellaneous. The last C-terminal 19 amino acids are not required for complex association and RNase activity.

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

Isoforms (2)

UniProt IDNamesCanonical?
Q969H6-11yes
Q969H6-22

RefSeq proteins (2): NP_057002, NP_937845 (=MANE)

Domains & families (InterPro)

IDNameType
IPR002759Pop5/Rpp14/Rnp2-likeFamily
IPR016819RNase_P/MRP_POP5Family
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 (6 total): sequence conflict 3, chain 1, modified residue 1, splice variant 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-Q969H6-F190.760.74

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): 154

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-6784531tRNA processing in the nucleus

MSigDB gene sets: 133 (showing top): GOBP_RIBOSOME_BIOGENESIS, GOMF_ENDONUCLEASE_ACTIVITY, GOMF_RNA_NUCLEASE_ACTIVITY, BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_DN, GOMF_NUCLEASE_ACTIVITY, GOBP_TRNA_METABOLIC_PROCESS, AATGGAG_MIR136, PUJANA_CHEK2_PCC_NETWORK, MUELLER_PLURINET, GOMF_RNA_ENDONUCLEASE_ACTIVITY, ROSS_LEUKEMIA_WITH_MLL_FUSIONS, BLALOCK_ALZHEIMERS_DISEASE_UP, TIEN_INTESTINE_PROBIOTICS_24HR_UP, MORF_AATF, GOBP_RIBONUCLEOPROTEIN_COMPLEX_BIOGENESIS

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

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

GO Cellular Component (7): ribonuclease MRP complex (GO:0000172), nucleoplasm (GO:0005654), nucleolar ribonuclease P complex (GO:0005655), nucleolus (GO:0005730), multimeric ribonuclease P complex (GO:0030681), nucleus (GO:0005634), ribonuclease P complex (GO:0030677)

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
endoribonuclease complex2
nuclear lumen2
tRNA 5’-end processing1
rRNA metabolic process1
ribosome biogenesis1
tRNA metabolic process1
tRNA-specific ribonuclease activity1
RNA endonuclease activity producing 5’-phosphomonoesters, hydrolytic mechanism1
RNA binding1
nucleic acid binding1
binding1
sno(s)RNA-containing ribonucleoprotein complex1
cellular anatomical structure1
nucleolus1
multimeric ribonuclease P complex1
nuclear protein-containing complex1
intracellular membraneless organelle1
ribonuclease P complex1
intracellular membrane-bounded organelle1
ribonucleoprotein complex1

Protein interactions and networks

STRING

804 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
POP5RPP30P78346998
POP5POP4O95707993
POP5RPP38P78345986
POP5RPP25Q9BUL9978
POP5RPP40O75818963
POP5POP7O75817891
POP5RPLP1P05386779
POP5PTERQ96BW5655
POP5PRORPO15091648
POP5DCLRE1AQ6PJP8591
POP5POP1Q99575544
POP5RPP25LQ8N5L8534
POP5RPP21Q9H633514
POP5COPS7BQ9H9Q2383
POP5RPP14O95059353

IntAct

87 interactions, top by confidence:

ABTypeScore
RPP25POP7psi-mi:“MI:0914”(association)0.810
RPP30POP5psi-mi:“MI:0915”(physical association)0.740
RPP30POP7psi-mi:“MI:0914”(association)0.730
CCDC102BPOP5psi-mi:“MI:0915”(physical association)0.720
TRAF1POP5psi-mi:“MI:0915”(physical association)0.720
POP5CEP44psi-mi:“MI:0915”(physical association)0.720
POP5CCDC102Bpsi-mi:“MI:0915”(physical association)0.720
POP5POP4psi-mi:“MI:0915”(physical association)0.670
POP4POP5psi-mi:“MI:0915”(physical association)0.670
RPP14POP5psi-mi:“MI:0915”(physical association)0.670
RPP25POP5psi-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
RELPOP5psi-mi:“MI:0915”(physical association)0.560
CAMK2BPOP5psi-mi:“MI:0915”(physical association)0.560
POP5KRT40psi-mi:“MI:0915”(physical association)0.560
POP5RELpsi-mi:“MI:0915”(physical association)0.560
POP5CAMK2Bpsi-mi:“MI:0915”(physical association)0.560
KRT40POP5psi-mi:“MI:0915”(physical association)0.560

BioGRID (61): POP5 (Two-hybrid), POP5 (Two-hybrid), POP5 (Two-hybrid), CCDC102B (Two-hybrid), CEP44 (Two-hybrid), KRT40 (Two-hybrid), POP5 (Affinity Capture-MS), POP5 (Affinity Capture-MS), POP5 (Affinity Capture-MS), POP5 (Affinity Capture-MS), POP5 (Affinity Capture-MS), POP5 (Affinity Capture-MS), POP5 (Affinity Capture-MS), POP5 (Affinity Capture-MS), RPP25 (Reconstituted Complex)

ESM2 similar proteins: A0A1L8F8I9, A2ARP1, B8B624, E7EXT2, F1S5L4, O95822, P0C644, P0C7N9, P28005, P38208, P41229, P53370, P97564, Q08BC6, Q14AI0, Q14BI7, Q1JQ92, Q24087, Q24169, Q28647, Q2KI89, Q32PH0, Q3MHU3, Q3U0M1, Q5BJI6, Q5GJ77, Q5JS54, Q61586, Q66I84, Q68F70, Q6AWV1, Q6GL75, Q6GMB0, Q6PD24, Q75B32, Q7XAM0, Q7Z2Z2, Q7ZU90, Q811G0, Q8BSA9

Diamond homologs: Q1JQ92, Q54EP3, Q5BJI6, Q969H6, Q9DB28, Q6AWV1, Q9UU90

SIGNOR signaling

2 interactions.

AEffectBMechanism
POP5“form complex”“Ribonuclease MRP complex”binding
POP5“form complex”“Nucleolar ribonuclease P complex”binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 37 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 processing6107.1×8e-10
tRNA processing in the nucleus878.8×5e-12
rRNA processing in the nucleus and cytosol648.2×8e-08
rRNA processing643.9×1e-07
Major pathway of rRNA processing in the nucleolus and cytosol618.5×1e-05
Metabolism of RNA816.7×3e-07

GO biological processes:

GO termPartnersFoldFDR
rRNA processing627.4×4e-06

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic1
Likely pathogenic0
Uncertain significance16
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (1)

Variant IDHGVSClassification
4682808GRCh37/hg19 12q24.21-24.33(chr12:116422123-133777902)x3Pathogenic

SpliceAI

748 predictions. Top by Δscore:

VariantEffectΔscore
12:120581338:CTTA:Cdonor_loss1.0000
12:120581339:TTAC:Tdonor_loss1.0000
12:120581340:TA:Tdonor_loss1.0000
12:120581341:A:ACdonor_gain1.0000
12:120581341:A:ATdonor_loss1.0000
12:120581342:C:CCdonor_gain1.0000
12:120579653:T:Cacceptor_gain0.9900
12:120581096:T:TAdonor_gain0.9900
12:120581097:C:Adonor_gain0.9900
12:120581106:C:CAdonor_gain0.9900
12:120581181:CGAGG:Cdonor_gain0.9900
12:120581342:CCT:Cdonor_gain0.9900
12:120579924:C:CCacceptor_gain0.9800
12:120581341:AC:Adonor_gain0.9800
12:120581342:CC:Cdonor_gain0.9800
12:120579410:CTC:Cacceptor_gain0.9700
12:120579652:C:CCacceptor_gain0.9700
12:120579759:C:CTdonor_gain0.9700
12:120579814:T:TAdonor_gain0.9700
12:120581102:AGCGC:Adonor_gain0.9700
12:120581111:G:Adonor_gain0.9700
12:120581160:C:CAdonor_gain0.9700
12:120581342:CCTG:Cdonor_gain0.9700
12:120581342:CCTGT:Cdonor_gain0.9700
12:120579651:ACTTT:Aacceptor_gain0.9600
12:120579652:CTTTC:Cacceptor_gain0.9600
12:120581152:T:TAdonor_gain0.9600
12:120579760:C:CTdonor_gain0.9500
12:120579656:C:CTacceptor_gain0.9300
12:120579776:C:Adonor_gain0.9300

AlphaMissense

1047 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
12:120581343:C:AR7M0.999
12:120579594:G:AT106I0.998
12:120581144:C:TG45D0.997
12:120579581:A:CC110W0.996
12:120579583:A:GC110R0.996
12:120579597:C:TG105D0.996
12:120579776:C:TG104E0.996
12:120579910:A:CN59K0.996
12:120579910:A:TN59K0.996
12:120581153:C:AG42V0.996
12:120581153:C:TG42E0.996
12:120581343:C:GR7T0.996
12:120581348:C:AK5N0.996
12:120581348:C:GK5N0.996
12:120579570:A:GL114P0.995
12:120579572:G:CF113L0.995
12:120579572:G:TF113L0.995
12:120579574:A:GF113L0.995
12:120579582:C:TC110Y0.995
12:120581247:A:GC11R0.995
12:120581257:C:AR7S0.995
12:120581257:C:GR7S0.995
12:120579591:A:TI107K0.994
12:120579546:A:GL122P0.993
12:120579579:T:GQ111P0.993
12:120579777:C:GG104R0.993
12:120579777:C:TG104R0.993
12:120579845:A:CL81R0.993
12:120579923:A:TV55D0.993
12:120581249:A:TL10H0.993

dbSNP variants (sampled 300 via entrez): RS1000106196 (12:120581524 A>C), RS1000492739 (12:120582506 A>C,G), RS1001534288 (12:120581355 C>A,G), RS1001604947 (12:120578475 G>A,T), RS1004872725 (12:120578695 G>A,C), RS1005010871 (12:120578873 T>C), RS1005310461 (12:120578416 G>A), RS1005554142 (12:120580731 G>A), RS1005891867 (12:120581774 C>T), RS1007574554 (12:120583288 C>A), RS1008747622 (12:120580334 A>G), RS1009056512 (12:120578990 A>G), RS1009111251 (12:120580608 TCAAA>T), RS1009673470 (12:120582791 C>G), RS1010356746 (12:120578824 T>C)

Disease associations

OMIM: gene MIM:609992 | 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
GCST004611_192High light scatter reticulocyte count2.000000e-83
GCST007576_31Chronotype3.000000e-09
GCST008759_15Intake of total sugars3.000000e-07

EFO canonical traits (3, from GWAS)

EFO IDTrait name
EFO:0007986reticulocyte count
EFO:0008328chronotype measurement
EFO:0010158sugar consumption measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects expression, affects cotreatment, increases expression5
Particulate Matterincreases abundance, affects cotreatment, decreases expression3
bisphenol Adecreases expression, increases expression2
Air Pollutantsincreases abundance, decreases expression2
Cyclosporinedecreases expression2
aristolochic acid Idecreases expression1
GSK-J4decreases expression1
FR900359increases phosphorylation1
dicrotophosdecreases expression1
arseniteincreases reaction, affects binding1
sodium arsenitedecreases expression1
cobaltous chloridedecreases expression1
potassium chromate(VI)affects cotreatment, decreases expression1
isobutyl alcoholaffects cotreatment, decreases expression, increases abundance1
epigallocatechin gallateaffects cotreatment, decreases expression1
di-n-butylphosphoric acidaffects expression1
deguelindecreases expression1
K 7174decreases expression1
erucylphospho-N,N,N-trimethylpropylammoniumdecreases expression1
abrinedecreases expression1
2-(1H-indazol-4-yl)-6-(4-methanesulfonylpiperazin-1-ylmethyl)-4-morpholin-4-ylthieno(3,2-d)pyrimidinedecreases expression, increases response to substance1
jinfukangaffects cotreatment, increases expression1
picoxystrobinincreases expression1
Resveratrolaffects cotreatment, increases expression1
Vorinostatincreases expression1
Leflunomidedecreases expression1
Cisplatinaffects cotreatment, increases expression1
Dichlorodiphenyl Dichloroethyleneincreases expression1
Dexamethasoneincreases expression1
Diurondecreases expression1

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_B3EAAbcam HEK293T POP5 KOTransformed cell lineFemale

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.