MRPL41

gene
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Also known as MRP-L27RPML27BMRPPIG3MRPL27mL41

Summary

MRPL41 (mitochondrial ribosomal protein L41, HGNC:14492) is a protein-coding gene on chromosome 9q34.3, encoding Large ribosomal subunit protein mL41 (Q8IXM3). Component of the mitochondrial ribosome large subunit. It is a selective cancer dependency (DepMap: 78.3% of cell lines).

Mammalian mitochondrial ribosomal proteins are encoded by nuclear genes and help in protein synthesis within the mitochondrion. Mitochondrial ribosomes (mitoribosomes) consist of a small 28S subunit and a large 39S subunit. They have an estimated 75% protein to rRNA composition compared to prokaryotic ribosomes, where this ratio is reversed. Another difference between mammalian mitoribosomes and prokaryotic ribosomes is that the latter contain a 5S rRNA. Among different species, the proteins comprising the mitoribosome differ greatly in sequence, and sometimes in biochemical properties, which prevents easy recognition by sequence homology. This gene encodes a 39S subunit protein that belongs to the YmL27 ribosomal protein family.

Source: NCBI Gene 64975 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 17 total
  • Cancer dependency (DepMap): dependent in 78.3% of screened cell lines
  • MANE Select transcript: NM_032477

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:14492
Approved symbolMRPL41
Namemitochondrial ribosomal protein L41
Location9q34.3
Locus typegene with protein product
StatusApproved
AliasesMRP-L27, RPML27, BMRP, PIG3, MRPL27, mL41
Ensembl geneENSG00000182154
Ensembl biotypeprotein_coding
OMIM611846
Entrez64975

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000371443

RefSeq mRNA: 1 — MANE Select: NM_032477 NM_032477

CCDS: CCDS7046

Canonical transcript exons

ENST00000371443 — 2 exons

ExonStartEnd
ENSE00001455236137552074137552555
ENSE00001455237137551879137551978

Expression profiles

Bgee: expression breadth ubiquitous, 256 present calls, max score 99.55.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 62.6359 / max 371.1834, expressed in 1820 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
9969962.63591820

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
apex of heartUBERON:000209899.55gold quality
left ventricle myocardiumUBERON:000656699.37gold quality
heart left ventricleUBERON:000208499.24gold quality
cardiac ventricleUBERON:000208299.23gold quality
right atrium auricular regionUBERON:000663199.19gold quality
heart right ventricleUBERON:000208099.15gold quality
cardiac atriumUBERON:000208199.15gold quality
mucosa of transverse colonUBERON:000499199.12gold quality
anterior cingulate cortexUBERON:000983598.99gold quality
myocardiumUBERON:000234998.97gold quality
caudate nucleusUBERON:000187398.95gold quality
putamenUBERON:000187498.94gold quality
hindlimb stylopod muscleUBERON:000425298.92gold quality
Brodmann (1909) area 9UBERON:001354098.91gold quality
right frontal lobeUBERON:000281098.88gold quality
cardiac muscle of right atriumUBERON:000337998.82gold quality
amygdalaUBERON:000187698.80gold quality
nucleus accumbensUBERON:000188298.80gold quality
gastrocnemiusUBERON:000138898.70gold quality
tibialis anteriorUBERON:000138598.63gold quality
right lobe of liverUBERON:000111498.47gold quality
heartUBERON:000094898.44gold quality
hypothalamusUBERON:000189898.36gold quality
dorsolateral prefrontal cortexUBERON:000983498.30gold quality
body of stomachUBERON:000116198.21gold quality
olfactory segment of nasal mucosaUBERON:000538698.12gold quality
quadriceps femorisUBERON:000137798.10gold quality
C1 segment of cervical spinal cordUBERON:000646998.06gold quality
muscle of legUBERON:000138398.05gold quality
left adrenal gland cortexUBERON:003582598.03gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 2.

ExperimentMarker?Max mean expression
E-MTAB-6819yes207.19
E-ANND-3yes15.91
E-MTAB-8559no680.00

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): DNMT1, ESR1, EZH2, LITAF, SSRP1, TP53, TP63, TP73, ZNF699

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 78.3% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 6)

  • BMRP is a mitochondrial ribosomal protein involved in the regulation of cell death by apoptosis, probably affecting pathways mediated by Bcl-2 and caspases. (PMID:15547950)
  • mitochondrial ribosomal protein L41 (MRPL41) is localized in the mitochondria, stabilizes the p53 protein, and enhances its translocation to the mitochondria, thereby inducing apoptosis. (PMID:16024796)
  • Overall, these results suggest that MRPL41 arrests the cell cycle by increasing the p21(WAF1/CIP1) and p27(Kip1) levels under the growth inhibitory conditions. (PMID:16256947)
  • region of BMRP required for the interaction with Bcl-2 is very relevant for the cell death-inducing activity of the protein (PMID:21253851)
  • Apoptosis-inducing ability of wild-type BMRP is blocked by Bcl-2 through several mechanisms. (PMID:22711503)
  • Nuclear-encoded mitochondrial MTO1 and MRPL41 are regulated in an opposite epigenetic mode based on estrogen receptor status in breast cancer. (PMID:24160266)

Cross-species orthologs

6 orthologs

OrganismSymbolGene ID
danio_reriomrpl41ENSDARG00000002264
mus_musculusMrpl41ENSMUSG00000036850
rattus_norvegicusMrpl41l1ENSRNOG00000034128
rattus_norvegicusMrpl41ENSRNOG00000080840
drosophila_melanogastermRpL41FBGN0034001
caenorhabditis_elegansWBGENE00015185

Protein

Protein identifiers

Large ribosomal subunit protein mL41Q8IXM3 (reviewed: Q8IXM3)

Alternative names: 39S ribosomal protein L41, mitochondrial, Bcl-2-interacting mitochondrial ribosomal protein L41, Cell proliferation-inducing gene 3 protein, MRP-L27 homolog

All UniProt accessions (1): Q8IXM3

UniProt curated annotations — full annotation on UniProt →

Function. Component of the mitochondrial ribosome large subunit. Also involved in apoptosis and cell cycle. Enhances p53/TP53 stability, thereby contributing to p53/TP53-induced apoptosis in response to growth-inhibitory condition. Enhances p53/TP53 translocation to the mitochondria. Has the ability to arrest the cell cycle at the G1 phase, possibly by stabilizing the CDKN1A and CDKN1B (p27Kip1) proteins.

Subunit / interactions. Component of the mitochondrial large ribosomal subunit (mt-LSU). Mature mammalian 55S mitochondrial ribosomes consist of a small (28S) and a large (39S) subunit. The 28S small subunit contains a 12S ribosomal RNA (12S mt-rRNA) and 30 different proteins. The 39S large subunit contains a 16S rRNA (16S mt-rRNA), a copy of mitochondrial valine transfer RNA (mt-tRNA(Val)), which plays an integral structural role, and 52 different proteins. Interacts with BCL2.

Subcellular location. Mitochondrion.

Tissue specificity. Present in kidney, liver, thymus and testis, and at lower level in brain and spleen (at protein level).

Similarity. Belongs to the mitochondrion-specific ribosomal protein mL41 family.

RefSeq proteins (1): NP_115866* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR019189Ribosomal_mL41Family

Pfam: PF09809

UniProt features (15 total): helix 6, strand 5, turn 2, transit peptide 1, chain 1

Structure

Experimental structures (PDB)

85 structures, top 30 by resolution.

PDBMethodResolution (Å)
7OF0ELECTRON MICROSCOPY2.2
7QI4ELECTRON MICROSCOPY2.21
8RRIELECTRON MICROSCOPY2.4
8QU5ELECTRON MICROSCOPY2.42
9OLFELECTRON MICROSCOPY2.46
7OF7ELECTRON MICROSCOPY2.5
7PO4ELECTRON MICROSCOPY2.56
6ZM6ELECTRON MICROSCOPY2.59
7O9MELECTRON MICROSCOPY2.6
7OF6ELECTRON MICROSCOPY2.6
9CN3ELECTRON MICROSCOPY2.62
7QI5ELECTRON MICROSCOPY2.63
7OF2ELECTRON MICROSCOPY2.7
7OF3ELECTRON MICROSCOPY2.7
7OF4ELECTRON MICROSCOPY2.7
9PR4ELECTRON MICROSCOPY2.77
9PRAELECTRON MICROSCOPY2.83
8ANYELECTRON MICROSCOPY2.85
6ZM5ELECTRON MICROSCOPY2.89
7QH7ELECTRON MICROSCOPY2.89
7ODRELECTRON MICROSCOPY2.9
7OF5ELECTRON MICROSCOPY2.9
8K2AELECTRON MICROSCOPY2.9
8OITELECTRON MICROSCOPY2.9
9PGLELECTRON MICROSCOPY2.9
9PGFELECTRON MICROSCOPY2.93
6VMIELECTRON MICROSCOPY2.96
6VLZELECTRON MICROSCOPY2.97
7QI6ELECTRON MICROSCOPY2.98
9PSMELECTRON MICROSCOPY2.98

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8IXM3-F191.260.80

Function

Pathways and Gene Ontology

Reactome pathways

7 pathways

IDPathway
R-HSA-5368286Mitochondrial translation initiation
R-HSA-5389840Mitochondrial translation elongation
R-HSA-5419276Mitochondrial translation termination
R-HSA-9937383Mitochondrial ribosome-associated quality control
R-HSA-392499Metabolism of proteins
R-HSA-5368287Mitochondrial translation
R-HSA-72766Translation

MSigDB gene sets: 273 (showing top): MODULE_255, RORA1_01, STARK_PREFRONTAL_CORTEX_22Q11_DELETION_DN, GOBP_MITOCHONDRIAL_TRANSLATION, MODULE_317, GOBP_TRANSLATION, WEI_MYCN_TARGETS_WITH_E_BOX, GOMF_STRUCTURAL_CONSTITUENT_OF_RIBOSOME, USF_01, KONDO_COLON_CANCER_HCP_WITH_H3K27ME1, GOCC_MITOCHONDRIAL_ENVELOPE, YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_13, USF_02, WONG_MITOCHONDRIA_GENE_MODULE, RASHI_RESPONSE_TO_IONIZING_RADIATION_6

GO Biological Process (3): translation (GO:0006412), apoptotic process (GO:0006915), mitochondrial translation (GO:0032543)

GO Molecular Function (3): RNA binding (GO:0003723), structural constituent of ribosome (GO:0003735), protein binding (GO:0005515)

GO Cellular Component (5): mitochondrion (GO:0005739), mitochondrial inner membrane (GO:0005743), mitochondrial large ribosomal subunit (GO:0005762), ribonucleoprotein complex (GO:1990904), ribosome (GO:0005840)

Reactome top-level categories

Rollup of top-3 pathways:

CategoryPathways
Mitochondrial translation4
Translation1
Metabolism of proteins1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
peptidyltransferase activity1
translational initiation1
translational elongation1
translational termination1
macromolecule biosynthetic process1
protein metabolic process1
protein biosynthetic process1
programmed cell death1
apoptotic signaling pathway1
execution phase of apoptosis1
mitochondrion1
translation1
mitochondrial gene expression1
nucleic acid binding1
structural molecule activity1
ribosome1
binding1
cytoplasm1
intracellular membrane-bounded organelle1
organelle inner membrane1
mitochondrial membrane1
organellar large ribosomal subunit1
mitochondrial ribosome1
mitochondrial protein-containing complex1
protein-containing complex1
intracellular membraneless organelle1

Protein interactions and networks

STRING

1917 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
MRPL41DAP3P51398730
MRPL41MRPL37Q9BZE1666
MRPL41MRPS30Q9NP92635
MRPL41MRPL11Q9Y3B7625
MRPL41MRPL12P52815625
MRPL41MRPS7Q9Y2R9623
MRPL41MRPS23Q9Y3D9606
MRPL41MRPL42Q9Y6G3585
MRPL41MRPL20Q9BYC9548
MRPL41MRPL34Q9BQ48529
MRPL41MRPL19P49406511
MRPL41MRPL13Q9BYD1495
MRPL41PPP1R21Q6ZMI0489
MRPL41A8MYK1A8MYK1475
MRPL41MRPL23Q16540475

IntAct

145 interactions, top by confidence:

ABTypeScore
CFTRESYT2psi-mi:“MI:0914”(association)0.710
MRPS30GTPBP10psi-mi:“MI:0914”(association)0.640
TMED8MRPL41psi-mi:“MI:0915”(physical association)0.560
NPKPNA6psi-mi:“MI:0914”(association)0.550
KSR2POLR3Apsi-mi:“MI:0914”(association)0.530
MRPL50GTPBP10psi-mi:“MI:0914”(association)0.530
MRPL10ZZEF1psi-mi:“MI:0914”(association)0.530
MRPL42GATCpsi-mi:“MI:0914”(association)0.530
MRPL38DUSP14psi-mi:“MI:0914”(association)0.530
MRPL28MRPL3psi-mi:“MI:0914”(association)0.530
MRPL41MRPL3psi-mi:“MI:0914”(association)0.530
MRPL2GTPBP10psi-mi:“MI:0914”(association)0.530
MRPL13GTPBP10psi-mi:“MI:0914”(association)0.530
MRPL18GTPBP10psi-mi:“MI:0914”(association)0.530
MRPL27MRPL33psi-mi:“MI:0914”(association)0.530
MRPL41TRIM63psi-mi:“MI:0915”(physical association)0.510
TRIM63MRPL41psi-mi:“MI:0915”(physical association)0.510
NDUFAB1MIEF1psi-mi:“MI:0915”(physical association)0.490
SMURF2MRPL41psi-mi:“MI:0915”(physical association)0.370

BioGRID (281): MRPL41 (Two-hybrid), MRPL41 (Two-hybrid), MRPL41 (Reconstituted Complex), MRPL41 (Affinity Capture-MS), MRPL41 (Affinity Capture-MS), MRPL41 (Affinity Capture-MS), MRPL41 (Affinity Capture-MS), MRPL41 (Affinity Capture-MS), MRPL41 (Co-fractionation), MRPL41 (Affinity Capture-MS), MRPL41 (Affinity Capture-MS), MRPL41 (Affinity Capture-MS), MRPL41 (Affinity Capture-MS), MRPL41 (Affinity Capture-MS), MRPL41 (Affinity Capture-MS)

ESM2 similar proteins: A6ZR80, G1TTQ5, O45946, O94658, P0CU36, P39032, P40078, P45633, P47964, P49181, P49630, P82673, Q09533, Q2M0G4, Q2YDF6, Q39724, Q3T171, Q498P2, Q498Z6, Q4PM12, Q502B0, Q54J69, Q5A2Y7, Q5BJX1, Q5M818, Q5R7L3, Q5RAZ9, Q60P81, Q66KU4, Q6CNC5, Q6DER2, Q6DJI4, Q6INF3, Q6Q415, Q7SEK9, Q8BJZ4, Q8IXM3, Q8SR96, Q8UW19, Q90YT2

Diamond homologs: P90993, Q502B0, Q5BJX1, Q6DJI4, Q6INF3, Q8IXM3, Q9CQN7, Q291A0, Q7JZM8, P36526

SIGNOR signaling

1 interactions.

AEffectBMechanism
MRPL41“form complex”“39S mitochondrial large ribosomal subunit”binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 132 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
Mitochondrial ribosome-associated quality control3545.2×2e-48
Mitochondrial translation3144.9×5e-43
Mitochondrial translation initiation3344.1×2e-45
Mitochondrial translation elongation3344.1×2e-45
Mitochondrial translation termination3338.1×4e-43
Translation3422.2×1e-35
Peptide chain elongation79.3×4e-04
Viral mRNA Translation79.3×4e-04

GO biological processes:

GO termPartnersFoldFDR
mitochondrial translation3554.8×1e-50
translation2523.1×5e-25
cytoplasmic translation711.7×4e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance17
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

68 predictions. Top by Δscore:

VariantEffectΔscore
9:137551978:GGTG:Gdonor_loss0.9900
9:137551979:G:GAdonor_loss0.9900
9:137551979:G:GGdonor_gain0.9900
9:137551980:T:Gdonor_loss0.9900
9:137551974:TCC:Tdonor_gain0.9800
9:137552068:CCGCA:Cacceptor_loss0.9700
9:137552069:CGCAG:Cacceptor_loss0.9700
9:137552070:GCAGG:Gacceptor_loss0.9700
9:137552071:CA:Cacceptor_loss0.9700
9:137552072:A:Cacceptor_loss0.9700
9:137552072:A:AGacceptor_gain0.9600
9:137552072:AG:Aacceptor_gain0.9600
9:137552073:G:GGacceptor_gain0.9600
9:137552073:GG:Gacceptor_gain0.9600
9:137552073:GGGC:Gacceptor_gain0.9600
9:137551977:AG:Adonor_gain0.9400
9:137551978:GG:Gdonor_gain0.9400
9:137551974:TCCAG:Tdonor_gain0.9000
9:137552072:AGG:Aacceptor_gain0.9000
9:137552073:GGG:Gacceptor_gain0.9000
9:137551917:TCG:Tdonor_gain0.8900
9:137552069:C:Aacceptor_gain0.8700
9:137552072:AGGGC:Aacceptor_gain0.8400
9:137552073:GGGCG:Gacceptor_gain0.8400
9:137551975:CCAG:Cdonor_gain0.8300
9:137551976:CAG:Cdonor_gain0.7900
9:137552223:TGGAG:Tacceptor_gain0.7500
9:137552224:GGAGG:Gacceptor_gain0.7500
9:137551979:G:Tdonor_gain0.6800
9:137552225:GA:Gacceptor_gain0.6300

AlphaMissense

893 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
9:137552283:T:CF68L0.955
9:137552285:C:AF68L0.955
9:137552285:C:GF68L0.955
9:137552229:T:CF50L0.950
9:137552231:C:AF50L0.950
9:137552231:C:GF50L0.950
9:137552355:T:CF92L0.941
9:137552357:C:AF92L0.941
9:137552357:C:GF92L0.941
9:137552266:T:AV62D0.940
9:137552153:G:CK24N0.928
9:137552153:G:TK24N0.928
9:137552463:T:CF128L0.927
9:137552465:C:AF128L0.927
9:137552465:C:GF128L0.927
9:137552380:T:AI100N0.924
9:137552356:T:CF92S0.909
9:137552464:T:CF128S0.892
9:137552148:A:CS23R0.891
9:137552150:C:AS23R0.891
9:137552150:C:GS23R0.891
9:137552260:T:CF60S0.883
9:137552450:G:CQ123H0.881
9:137552450:G:TQ123H0.881
9:137552484:T:CF135L0.879
9:137552486:C:AF135L0.879
9:137552486:C:GF135L0.879
9:137552206:G:AG42D0.871
9:137552142:T:AW21R0.867
9:137552142:T:CW21R0.867

dbSNP variants (sampled 300 via entrez): RS1001177799 (9:137552474 C>G,T), RS1001462123 (9:137552775 G>T), RS1001966535 (9:137552735 G>A), RS1002828601 (9:137550686 A>G), RS1002896465 (9:137552895 A>G), RS1003162830 (9:137551728 C>A,G), RS1003229968 (9:137551606 G>A), RS1003639246 (9:137551453 A>G), RS1004526216 (9:137553049 G>A), RS1005025965 (9:137552823 A>G), RS1006298499 (9:137550254 G>C), RS1006659312 (9:137551216 G>A), RS1007990293 (9:137552006 C>T), RS1009487716 (9:137552910 G>A), RS1010088684 (9:137551735 G>A,C)

Disease associations

OMIM: gene MIM:611846 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects expression, increases expression, increases methylation5
Acetaminophenaffects cotreatment, decreases expression, increases expression3
bisphenol Aaffects expression, increases abundance, decreases methylation, affects cotreatment2
sodium arseniteincreases expression, decreases expression2
Particulate Matterdecreases expression, increases abundance, affects cotreatment, increases expression2
aristolochic acid Iincreases expression1
bisphenol Fincreases expression1
ginger extractaffects cotreatment, affects expression, increases abundance1
lead acetateincreases expression1
arseniteaffects binding, increases reaction1
4-(N-methyl-N-nitrosamino)-1-(3-pyridyl)-1-butanoneaffects cotreatment, increases expression, decreases reaction1
pinosylvindecreases expression1
di-n-butylphosphoric acidaffects expression1
CGP 52608affects binding, increases reaction1
corosolic aciddecreases expression1
K 7174decreases expression1
bisphenol Sincreases expression1
Temozolomideincreases expression1
Air Pollutantsincreases abundance, decreases expression1
Ethanolincreases abundance, increases expression, affects cotreatment1
Atrazinedecreases expression1
Benzo(a)pyreneaffects cotreatment, increases expression, decreases reaction1
Catechinaffects cotreatment, decreases reaction, increases expression1
Dactinomycinaffects localization, increases reaction, increases stability1
Gasolineaffects cotreatment, increases abundance, increases expression1
Lipopolysaccharidesaffects cotreatment, decreases expression1
Oils, Volatileincreases abundance, affects cotreatment, affects expression1
Polycyclic Aromatic Hydrocarbonsincreases abundance, increases expression, affects cotreatment1
Ribonucleotidesaffects binding1
Smokedecreases 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.