MRPS15

gene
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Also known as FLJ11564uS15m

Summary

MRPS15 (mitochondrial ribosomal protein S15, HGNC:14504) is a protein-coding gene on chromosome 1p34.3, encoding Small ribosomal subunit protein uS15m (P82914). It is a selective cancer dependency (DepMap: 17.7% 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 28S subunit protein that belongs to the ribosomal protein S15P family. The encoded protein is more than two times the size of its E. coli counterpart, with the 12S rRNA binding sites conserved. Between human and mouse, the encoded protein is the least conserved among small subunit ribosomal proteins. Pseudogenes corresponding to this gene are found on chromosomes 15q and 19q.

Source: NCBI Gene 64960 — RefSeq curated summary.

At a glance

  • GWAS associations: 3
  • Clinical variants (ClinVar): 55 total
  • Cancer dependency (DepMap): dependent in 17.7% of screened cell lines
  • MANE Select transcript: NM_031280

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:14504
Approved symbolMRPS15
Namemitochondrial ribosomal protein S15
Location1p34.3
Locus typegene with protein product
StatusApproved
AliasesFLJ11564, uS15m
Ensembl geneENSG00000116898
Ensembl biotypeprotein_coding
OMIM611979
Entrez64960

Gene structure

Transcript identifiers

Ensembl transcripts: 14 — 11 protein_coding, 3 protein_coding_CDS_not_defined

ENST00000373116, ENST00000462067, ENST00000477040, ENST00000488606, ENST00000869082, ENST00000869083, ENST00000869084, ENST00000869085, ENST00000917996, ENST00000917997, ENST00000917998, ENST00000917999, ENST00000918000, ENST00000918001

RefSeq mRNA: 1 — MANE Select: NM_031280 NM_031280

CCDS: CCDS411

Canonical transcript exons

ENST00000373116 — 8 exons

ExonStartEnd
ENSE000008612633645792336457981
ENSE000008612643646069236460776
ENSE000008612653646126436461312
ENSE000010791853646380636463850
ENSE000012005983646208836462163
ENSE000014595413646414636464384
ENSE000018507293645571836455925
ENSE000034777233645618736456378

Expression profiles

Bgee: expression breadth ubiquitous, 283 present calls, max score 99.21.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 68.8544 / max 414.3116, expressed in 1826 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter IDTPM avgSamples expressed
1174061.52981824
117393.81091612
117412.59841395
117340.6169312
117380.222391
117330.076214

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
biceps brachiiUBERON:000150799.21gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451199.17gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450299.12gold quality
body of tongueUBERON:001187699.11gold quality
spermCL:000001998.88gold quality
lateral nuclear group of thalamusUBERON:000273698.80gold quality
heart right ventricleUBERON:000208098.79gold quality
parotid glandUBERON:000183198.68gold quality
gingival epitheliumUBERON:000194998.66gold quality
left testisUBERON:000453398.64gold quality
adult organismUBERON:000702398.57gold quality
right testisUBERON:000453498.51gold quality
pharyngeal mucosaUBERON:000035598.48gold quality
gingivaUBERON:000182898.46gold quality
mammalian vulvaUBERON:000099798.45gold quality
hindlimb stylopod muscleUBERON:000425298.43gold quality
superior surface of tongueUBERON:000737198.26gold quality
substantia nigra pars compactaUBERON:000196598.24gold quality
vena cavaUBERON:000408798.19gold quality
gastrocnemiusUBERON:000138898.18gold quality
pericardiumUBERON:000240798.18gold quality
ponsUBERON:000098898.05gold quality
muscle of legUBERON:000138397.99gold quality
cardia of stomachUBERON:000116297.98gold quality
substantia nigra pars reticulataUBERON:000196697.89gold quality
apex of heartUBERON:000209897.88gold quality
renal medullaUBERON:000036297.74gold quality
muscle organUBERON:000163097.74gold quality
lateral globus pallidusUBERON:000247697.65gold quality
pylorusUBERON:000116697.62gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes15.79
E-HCAD-5no2.23

Regulation

Is transcription factor: no

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 17.7% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 1)

  • Mitochondrial Ribosomal Protein MRPS15 Is a Component of Cytosolic Ribosomes and Regulates Translation in Stressed Cardiomyocytes. (PMID:38542224)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriomrps15ENSDARG00000109289
mus_musculusMrps15ENSMUSG00000028861
rattus_norvegicusMrps15ENSRNOG00000008279
drosophila_melanogasterbonsaiFBGN0026261
caenorhabditis_elegansmrps-15WBGENE00010624

Protein

Protein identifiers

Small ribosomal subunit protein uS15mP82914 (reviewed: P82914)

Alternative names: 28S ribosomal protein S15, mitochondrial

All UniProt accessions (1): P82914

UniProt curated annotations — full annotation on UniProt →

Subunit / interactions. Component of the mitochondrial small ribosomal subunit (mt-SSU). 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 METTL17.

Subcellular location. Mitochondrion matrix.

Similarity. Belongs to the universal ribosomal protein uS15 family.

RefSeq proteins (1): NP_112570* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000589Ribosomal_uS15Family
IPR005290Ribosomal_uS15_bactFamily
IPR009068uS15_NS1_RNA-bd_sfHomologous_superfamily
IPR052137uS15_ribosomalFamily

Pfam: PF00312

UniProt features (14 total): helix 9, transit peptide 1, chain 1, region of interest 1, sequence conflict 1, strand 1

Structure

Experimental structures (PDB)

77 structures, top 30 by resolution.

PDBMethodResolution (Å)
7QI4ELECTRON MICROSCOPY2.21
8CSSELECTRON MICROSCOPY2.36
7P2EELECTRON MICROSCOPY2.4
8RRIELECTRON MICROSCOPY2.4
9OLFELECTRON MICROSCOPY2.46
9OJMELECTRON MICROSCOPY2.5
8CSQELECTRON MICROSCOPY2.54
8CSRELECTRON MICROSCOPY2.54
6ZM6ELECTRON MICROSCOPY2.59
7QI5ELECTRON MICROSCOPY2.63
8CSPELECTRON MICROSCOPY2.66
7PNXELECTRON MICROSCOPY2.76
8ANYELECTRON MICROSCOPY2.85
8CSTELECTRON MICROSCOPY2.85
6ZM5ELECTRON MICROSCOPY2.89
7PO0ELECTRON MICROSCOPY2.9
8K2AELECTRON MICROSCOPY2.9
9PGLELECTRON MICROSCOPY2.9
7PO1ELECTRON MICROSCOPY2.92
7PO3ELECTRON MICROSCOPY2.92
9PGFELECTRON MICROSCOPY2.93
6VMIELECTRON MICROSCOPY2.96
6RW4ELECTRON MICROSCOPY2.97
6VLZELECTRON MICROSCOPY2.97
7QI6ELECTRON MICROSCOPY2.98
8QRNELECTRON MICROSCOPY2.98
9PSMELECTRON MICROSCOPY2.98
8OISELECTRON MICROSCOPY3
9G5CELECTRON MICROSCOPY3
9G5DELECTRON MICROSCOPY3

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P82914-F179.290.65

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: 165 (showing top): LU_IL4_SIGNALING, MODULE_255, GAUSSMANN_MLL_AF4_FUSION_TARGETS_C_UP, GOBP_MITOCHONDRIAL_TRANSLATION, MODULE_317, MONNIER_POSTRADIATION_TUMOR_ESCAPE_UP, GOBP_TRANSLATION, WEI_MYCN_TARGETS_WITH_E_BOX, WANG_LMO4_TARGETS_DN, GOMF_STRUCTURAL_CONSTITUENT_OF_RIBOSOME, chr1p34, GOCC_MITOCHONDRIAL_ENVELOPE, WONG_MITOCHONDRIA_GENE_MODULE, ROSTY_CERVICAL_CANCER_PROLIFERATION_CLUSTER, GOCC_RIBOSOME

GO Biological Process (2): translation (GO:0006412), 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 (9): nucleoplasm (GO:0005654), nucleolus (GO:0005730), mitochondrion (GO:0005739), mitochondrial inner membrane (GO:0005743), mitochondrial matrix (GO:0005759), mitochondrial small ribosomal subunit (GO:0005763), mitochondrial ribosome (GO:0005761), ribosome (GO:0005840), ribonucleoprotein complex (GO:1990904)

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
mitochondrion2
nuclear lumen2
intracellular membraneless organelle2
peptidyltransferase activity1
translational initiation1
translational elongation1
translational termination1
macromolecule biosynthetic process1
protein metabolic process1
protein biosynthetic process1
translation1
mitochondrial gene expression1
nucleic acid binding1
structural molecule activity1
ribosome1
binding1
cellular anatomical structure1
cytoplasm1
intracellular membrane-bounded organelle1
organelle inner membrane1
mitochondrial membrane1
intracellular organelle lumen1
organellar small ribosomal subunit1
mitochondrial ribosome1
mitochondrial protein-containing complex1
organellar ribosome1
mitochondrial matrix1
protein-containing complex1

Protein interactions and networks

STRING

4410 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
MRPS15MRPL13Q9BYD1666
MRPS15MRPS16Q9Y3D3591
MRPS15MRPS21P82921588
MRPS15MRPS5P82675574
MRPS15MRPS7Q9Y2R9573
MRPS15MRPL11Q9Y3B7568
MRPS15MRPS11P82912559
MRPS15MRPS9P82933558
MRPS15MRPL34Q9BQ48535
MRPS15MRPL20Q9BYC9534
MRPS15MRPL21Q7Z2W9534
MRPS15MRPS10P82664531
MRPS15RPS9P46781522
MRPS15MRPL12P52815521
MRPS15MRPL24Q96A35516

IntAct

145 interactions, top by confidence:

ABTypeScore
MRPS27MRPS15psi-mi:“MI:0915”(physical association)0.740
MRPS27MRPS15psi-mi:“MI:0403”(colocalization)0.740
CFTRESYT2psi-mi:“MI:2364”(proximity)0.710
ESR1TRIM24psi-mi:“MI:0914”(association)0.640
LIN28AIGF2BP3psi-mi:“MI:0914”(association)0.640
MRPS15PTCD3psi-mi:“MI:0915”(physical association)0.560
NPKPNA6psi-mi:“MI:0914”(association)0.550
RPS6IPO7psi-mi:“MI:0914”(association)0.530
MRPS24ZZEF1psi-mi:“MI:0914”(association)0.530
MRPS15MRPS14psi-mi:“MI:0914”(association)0.530
TRMT10BMRPS14psi-mi:“MI:0914”(association)0.530
TMA16TNPO2psi-mi:“MI:0914”(association)0.530
MRPS18BMRPS14psi-mi:“MI:0914”(association)0.530
MRPS34ZZEF1psi-mi:“MI:0914”(association)0.530
MRPS18CMRPS14psi-mi:“MI:0914”(association)0.530
ZFC3H1HNRNPCL1psi-mi:“MI:0914”(association)0.530
MRPS15PRKACGpsi-mi:“MI:0914”(association)0.530
MRPS34MRPS12psi-mi:“MI:0914”(association)0.530
MRPS11MRPS14psi-mi:“MI:0914”(association)0.530
ABT1ZNF316psi-mi:“MI:0914”(association)0.530
AURKAIP1NRDCpsi-mi:“MI:0914”(association)0.480
ESR2FBLL1psi-mi:“MI:0914”(association)0.460
EXOC8MRPS15psi-mi:“MI:0915”(physical association)0.400
REXO1L1PMRPS15psi-mi:“MI:0915”(physical association)0.400
MRPS15H1-1psi-mi:“MI:0915”(physical association)0.400

BioGRID (218): MRPS15 (Affinity Capture-MS), MRPS15 (Affinity Capture-MS), MRPS15 (Affinity Capture-MS), MRPS15 (Affinity Capture-MS), MRPS15 (Affinity Capture-MS), MRPS15 (Affinity Capture-MS), MRPS15 (Affinity Capture-MS), MRPS15 (Affinity Capture-MS), MRPS15 (Affinity Capture-MS), MRPS15 (Affinity Capture-MS), MRPS15 (Affinity Capture-MS), MRPS15 (Affinity Capture-MS), MRPS15 (Affinity Capture-MS), MRPS15 (Affinity Capture-MS), MRPS15 (Affinity Capture-MS)

ESM2 similar proteins: A0A1D8PF11, A1ZAB5, A8PJX4, B0W2S0, B2GUB3, B3MB79, B3MIW0, B4KT50, B4LQ23, B4P6P7, F4HR03, F7AEX0, G1STW0, O13672, O57592, O76732, P03373, P0DJ14, P0DKK7, P12970, P17076, P29453, P32429, P35685, P46223, P49692, P62424, P62425, P82914, Q17N71, Q1LUC3, Q2TBQ5, Q3TPE9, Q3UFY4, Q4R5C2, Q54ZD1, Q5ANA1, Q5XI37, Q5ZMD2, Q7PZD5

Diamond homologs: A0RPX5, A1R0M9, A1VZL9, A3N113, A4XL65, A5I4I8, A5IMM9, A5IY18, A5N847, A5UC84, A5UEY4, A6LJ39, A6LSQ9, A6VQB6, A6W814, A7FVY8, A7GG01, A7GXT2, A7H3P9, A7H9F7, A7I1V7, A7ZEC8, A8F724, A8FLT4, A9BH72, A9KNL0, B0BPU4, B0SH21, B0SQH7, B0T174, B0THS1, B0USL5, B1HR10, B1II44, B1KWK2, B1LBY1, B1ZS99, B2A3A2, B2S1E8, B2S4C4

SIGNOR signaling

1 interactions.

AEffectBMechanism
MRPS15“form complex”“28S mitochondrial small ribosomal subunit”binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 166 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 translation initiation2022.7×1e-19
Mitochondrial translation elongation2022.7×1e-19
Mitochondrial translation1822.1×9e-18
Mitochondrial ribosome-associated quality control2021.9×1e-19
Mitochondrial translation termination2019.6×1e-18
Translation2111.6×6e-15
Signaling by ROBO receptors77.8×2e-03
Metabolism of RNA114.1×5e-03

GO biological processes:

GO termPartnersFoldFDR
mitochondrial translation2024.0×2e-19
translation1611.3×4e-10
RNA processing710.6×1e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance35
Likely benign5
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1117 predictions. Top by Δscore:

VariantEffectΔscore
1:36455926:C:CAacceptor_loss1.0000
1:36455926:C:CCacceptor_gain1.0000
1:36455932:A:ACacceptor_gain1.0000
1:36455932:A:Cacceptor_gain1.0000
1:36456204:T:TAdonor_gain1.0000
1:36456374:TTGTC:Tacceptor_gain1.0000
1:36456375:TGTC:Tacceptor_gain1.0000
1:36456376:GTC:Gacceptor_gain1.0000
1:36456376:GTCCT:Gacceptor_loss1.0000
1:36456377:TC:Tacceptor_gain1.0000
1:36456377:TCCTG:Tacceptor_loss1.0000
1:36456378:CC:Cacceptor_gain1.0000
1:36456378:CCT:Cacceptor_loss1.0000
1:36456379:C:CCacceptor_gain1.0000
1:36456379:C:CGacceptor_loss1.0000
1:36456380:T:Aacceptor_loss1.0000
1:36457919:TTAC:Tdonor_loss1.0000
1:36457920:TACC:Tdonor_loss1.0000
1:36457922:CC:Cdonor_loss1.0000
1:36457979:TAA:Tacceptor_gain1.0000
1:36457982:C:CCacceptor_gain1.0000
1:36460700:T:TAdonor_gain1.0000
1:36460772:TCCTT:Tacceptor_gain1.0000
1:36460773:CCTTC:Cacceptor_gain1.0000
1:36460774:CTT:Cacceptor_gain1.0000
1:36460775:TT:Tacceptor_gain1.0000
1:36460775:TTC:Tacceptor_loss1.0000
1:36460776:TCT:Tacceptor_loss1.0000
1:36460777:C:CAacceptor_loss1.0000
1:36460777:C:CCacceptor_gain1.0000

AlphaMissense

1670 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
1:36456289:A:CF178L0.977
1:36456289:A:TF178L0.977
1:36456291:A:GF178L0.977
1:36456334:C:AR163S0.965
1:36456334:C:GR163S0.965
1:36456311:C:GR171P0.957
1:36456312:G:TR171S0.956
1:36456362:C:GR154P0.948
1:36456205:C:AK206N0.945
1:36456205:C:GK206N0.945
1:36456376:G:CD149E0.944
1:36456376:G:TD149E0.944
1:36455920:G:CF214L0.941
1:36455920:G:TF214L0.941
1:36455922:A:GF214L0.941
1:36456314:A:GL170P0.939
1:36456364:T:AK153N0.933
1:36456364:T:GK153N0.933
1:36456356:A:GL156P0.931
1:36456378:C:GD149H0.926
1:36457960:A:GI136T0.915
1:36456377:T:GD149A0.913
1:36460694:C:GR128P0.911
1:36456323:A:TL167H0.909
1:36456335:C:GR163T0.906
1:36456323:A:GL167P0.902
1:36456277:G:CC182W0.899
1:36456338:T:GQ162P0.899
1:36456290:A:CF178C0.889
1:36456363:G:TR154S0.887

dbSNP variants (sampled 300 via entrez): RS1000266823 (1:36460209 G>A,T), RS1000790562 (1:36465679 T>C), RS1000799319 (1:36461658 C>A), RS1001065410 (1:36455495 C>T), RS1001395682 (1:36460042 G>A), RS1001529972 (1:36459720 A>G), RS1001738640 (1:36465436 G>A), RS1003070903 (1:36458370 A>T), RS1003239783 (1:36465128 T>C), RS1003277832 (1:36464237 C>G), RS1003413506 (1:36459267 G>A,T), RS1003822981 (1:36463887 A>C), RS1004402157 (1:36463828 G>A), RS1004466467 (1:36463421 TG>T), RS1004538364 (1:36463666 A>C)

Disease associations

OMIM: gene MIM:611979 | 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
GCST001017_4Diabetic retinopathy4.000000e-06
GCST007007_1Cerebrospinal fluid t-tau levels2.000000e-06
GCST007008_1Cerebrospinal fluid p-tau levels5.000000e-07

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0004760t-tau measurement
EFO:0004763p-tau measurement

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
bisphenol Adecreases expression2
Acetaminophenaffects cotreatment, decreases expression2
FR900359decreases phosphorylation1
TAK-243increases sumoylation1
triphenyl phosphateaffects expression1
arseniteaffects binding, increases reaction1
di-n-butylphosphoric acidaffects expression1
perfluorooctane sulfonic acidincreases expression1
chloropicrinincreases expression1
perfluoro-n-nonanoic acidincreases expression1
bisphenol Sincreases expression1
(+)-JQ1 compounddecreases expression1
bisphenol AFincreases expression1
Benzo(a)pyreneaffects methylation1
Formaldehydedecreases expression1
Lipopolysaccharidesaffects cotreatment, decreases expression1
Ribonucleotidesaffects binding1
Smokedecreases expression1
Tobacco Smoke Pollutionincreases expression1
Urethanedecreases expression1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxideincreases expression1
Paclitaxelaffects response to substance1
Sodium Seleniteincreases expression1
Lactic Aciddecreases expression1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.

  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): diabetic retinopathy