MRPS6

gene
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Also known as MRP-S6RPMS6bS6m

Summary

MRPS6 (mitochondrial ribosomal protein S6, HGNC:14051) is a protein-coding gene on chromosome 21q22.11, encoding Small ribosomal subunit protein bS6m (P82932). It is a selective cancer dependency (DepMap: 57.6% 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 S6P family. Pseudogenes corresponding to this gene are found on chromosomes 1p and 12q.

Source: NCBI Gene 64968 — RefSeq curated summary.

At a glance

  • GWAS associations: 5
  • Clinical variants (ClinVar): 62 total
  • Cancer dependency (DepMap): dependent in 57.6% of screened cell lines
  • MANE Select transcript: NM_032476

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:14051
Approved symbolMRPS6
Namemitochondrial ribosomal protein S6
Location21q22.11
Locus typegene with protein product
StatusApproved
AliasesMRP-S6, RPMS6, bS6m
Ensembl geneENSG00000243927
Ensembl biotypeprotein_coding
OMIM611973
Entrez64968

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 3 protein_coding_CDS_not_defined, 2 nonsense_mediated_decay, 1 protein_coding, 1 retained_intron

ENST00000362077, ENST00000399312, ENST00000477091, ENST00000482679, ENST00000483977, ENST00000488492, ENST00000715810

RefSeq mRNA: 1 — MANE Select: NM_032476 NM_032476

CCDS: CCDS33548

Canonical transcript exons

ENST00000399312 — 3 exons

ExonStartEnd
ENSE000015374883407357834073745
ENSE000034910913414240834143030
ENSE000035977563412534134125480

Expression profiles

Bgee: expression breadth ubiquitous, 255 present calls, max score 99.51.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 4.5590 / max 44.3196, expressed in 1679 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter IDTPM avgSamples expressed
18891196.70101828
1889102.09971145
1889092.05961205
1889170.3997208

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
renal medullaUBERON:000036299.51gold quality
metanephros cortexUBERON:001053398.26gold quality
kidney epitheliumUBERON:000481998.15gold quality
left lobe of thyroid glandUBERON:000112097.90gold quality
deciduaUBERON:000245097.90gold quality
thyroid glandUBERON:000204697.75gold quality
metanephrosUBERON:000008197.54gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099197.46gold quality
adult mammalian kidneyUBERON:000008297.44gold quality
right lobe of thyroid glandUBERON:000111997.42gold quality
tibial arteryUBERON:000761097.31gold quality
popliteal arteryUBERON:000225097.30gold quality
right adrenal gland cortexUBERON:003582797.29gold quality
right coronary arteryUBERON:000162597.17gold quality
tibial nerveUBERON:000132397.13gold quality
aortaUBERON:000094797.12gold quality
dorsal root ganglionUBERON:000004497.11gold quality
descending thoracic aortaUBERON:000234597.11gold quality
cortical plateUBERON:000534397.11gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451197.05gold quality
trigeminal ganglionUBERON:000167597.03gold quality
right adrenal glandUBERON:000123396.96gold quality
ascending aortaUBERON:000149696.92gold quality
thoracic aortaUBERON:000151596.91gold quality
calcaneal tendonUBERON:000370196.86gold quality
ventricular zoneUBERON:000305396.76gold quality
left coronary arteryUBERON:000162696.69gold quality
coronary arteryUBERON:000162196.55gold quality
pigmented layer of retinaUBERON:000178296.52gold quality
saphenous veinUBERON:000731896.51gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 3.

ExperimentMarker?Max mean expression
E-MTAB-8142yes35.20
E-GEOD-125970yes14.31
E-MTAB-10485no712.91
E-ANND-3no0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

39 targeting MRPS6, 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-1252-5P100.0069.802774
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-548P99.9872.253784
HSA-MIR-3692-3P99.9870.272139
HSA-MIR-548AN99.9770.912817
HSA-MIR-570-3P99.9672.414910
HSA-MIR-3912-5P99.9566.11925
HSA-MIR-6768-5P99.9267.361942
HSA-MIR-568099.9169.833421
HSA-MIR-10527-5P99.9172.283754
HSA-MIR-4697-3P99.8967.091123
HSA-MIR-369-3P99.8570.522264
HSA-MIR-202-3P99.8471.411290
HSA-MIR-6515-3P99.8268.191933
HSA-MIR-374C-5P99.8072.062910
HSA-MIR-655-3P99.8072.192909
HSA-MIR-548AJ-5P99.7871.123085
HSA-MIR-548F-5P99.7871.023093
HSA-MIR-548G-5P99.7871.123085
HSA-MIR-548X-5P99.7871.123085
HSA-MIR-556-3P99.7468.751203
HSA-MIR-368599.6268.831621
HSA-MIR-425-5P99.5967.67900
HSA-MIR-467299.5071.582893
HSA-MIR-65799.4866.02848
HSA-MIR-330-3P99.4169.952521
HSA-MIR-888-5P99.3070.151855
HSA-MIR-6768-3P99.1467.381319
HSA-MIR-806699.0568.661532
HSA-MIR-3117-5P99.0467.93618

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 57.6% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 2)

  • Mitochondrial ribosomal small subunit proteins (MRPS) MRPS6 and MRPS23 show dysregulation in breast cancer affecting tumorigenic cellular processes. (PMID:33964376)
  • MRPS6 modulates glucose-stimulated insulin secretion in mouse islet cells through mitochondrial unfolded protein response. (PMID:37758822)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriomrps6ENSDARG00000039543
mus_musculusMrps6ENSMUSG00000039680
rattus_norvegicusMrps6ENSRNOG00000059381

Protein

Protein identifiers

Small ribosomal subunit protein bS6mP82932 (reviewed: P82932)

Alternative names: 28S ribosomal protein S6, mitochondrial

All UniProt accessions (1): P82932

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.

Subcellular location. Mitochondrion.

Similarity. Belongs to the bacterial ribosomal protein bS6 family.

RefSeq proteins (1): NP_115865* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000529Ribosomal_bS6Family
IPR014717Transl_elong_EF1B/ribsomal_bS6Homologous_superfamily
IPR035980Ribosomal_bS6_sfHomologous_superfamily

Pfam: PF01250

UniProt features (9 total): strand 4, helix 3, chain 1, turn 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-P82932-F192.500.81

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: 175 (showing top): HONMA_DOCETAXEL_RESISTANCE, GCANCTGNY_MYOD_Q6, GOBP_MITOCHONDRIAL_TRANSLATION, IVANOVA_HEMATOPOIESIS_LATE_PROGENITOR, CAGCTG_AP4_Q5, GOBP_TRANSLATION, NFKB_C, GOMF_STRUCTURAL_CONSTITUENT_OF_RIBOSOME, GGARNTKYCCA_UNKNOWN, SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_UP, GOCC_MITOCHONDRIAL_ENVELOPE, ZHOU_INFLAMMATORY_RESPONSE_LIVE_DN, AACTTT_UNKNOWN, DOUGLAS_BMI1_TARGETS_UP, chr21q22

GO Biological Process (2): translation (GO:0006412), mitochondrial translation (GO:0032543)

GO Molecular Function (4): structural constituent of ribosome (GO:0003735), small ribosomal subunit rRNA binding (GO:0070181), protein binding (GO:0005515), rRNA binding (GO:0019843)

GO Cellular Component (6): mitochondrion (GO:0005739), mitochondrial inner membrane (GO:0005743), mitochondrial small ribosomal subunit (GO:0005763), small ribosomal subunit (GO:0015935), 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
peptidyltransferase activity1
translational initiation1
translational elongation1
translational termination1
macromolecule biosynthetic process1
protein metabolic process1
protein biosynthetic process1
mitochondrion1
translation1
mitochondrial gene expression1
structural molecule activity1
ribosome1
rRNA binding1
binding1
RNA binding1
cytoplasm1
intracellular membrane-bounded organelle1
organelle inner membrane1
mitochondrial membrane1
organellar small ribosomal subunit1
mitochondrial ribosome1
mitochondrial protein-containing complex1
ribosomal subunit1
intracellular membraneless organelle1
protein-containing complex1

Protein interactions and networks

STRING

2369 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
MRPS6SLC5A3P53794637
MRPS6TMEM50BP56557585
MRPS6WDR12Q9GZL7580
MRPS6PHACTR1Q9C0D0571
MRPS6MRPS10P82664561
MRPS6DONSONQ9NYP3559
MRPS6MRPS18CQ9Y3D5555
MRPS6MRPL22Q9NWU5552
MRPS6MIA3Q5JRA6544
MRPS6MRPL1Q9BYD6534
MRPS6MRPS16Q9Y3D3530
MRPS6MRPS5P82675517
MRPS6DOP1BQ9Y3R5517
MRPS6KCNE2Q9Y6J6507
MRPS6MRPS14O60783504

IntAct

98 interactions, top by confidence:

ABTypeScore
FBLNOP56psi-mi:“MI:0914”(association)0.800
STAT5BMRPS6psi-mi:“MI:0915”(physical association)0.670
ESR1TRIM24psi-mi:“MI:0914”(association)0.640
IGF2BP1IGF2BP3psi-mi:“MI:0914”(association)0.640
MRPS6MKRN3psi-mi:“MI:0915”(physical association)0.560
MKRN3MRPS6psi-mi:“MI:0915”(physical association)0.560
MRPS6LNX1psi-mi:“MI:0915”(physical association)0.560
MRPS6taxpsi-mi:“MI:0915”(physical association)0.560
taxMRPS6psi-mi:“MI:0915”(physical association)0.560
NPKPNA6psi-mi:“MI:0914”(association)0.550
STAT5AMRPS6psi-mi:“MI:0915”(physical association)0.550
MRPS6STAT5Apsi-mi:“MI:0914”(association)0.550
RPS6IPO7psi-mi:“MI:0914”(association)0.530
MRPS15MRPS14psi-mi:“MI:0914”(association)0.530
MRPS18BMRPS14psi-mi:“MI:0914”(association)0.530
MRPS34MRPS12psi-mi:“MI:0914”(association)0.530
MRPS11MRPS14psi-mi:“MI:0914”(association)0.530
SRPK2MRPS6psi-mi:“MI:0217”(phosphorylation reaction)0.440
MRPS6psi-mi:“MI:0915”(physical association)0.370
MRPS6CFAP418psi-mi:“MI:0915”(physical association)0.370
SREBF2MRPS6psi-mi:“MI:0915”(physical association)0.370
MRPS6RNF181psi-mi:“MI:0915”(physical association)0.370
MRPL50MRPL43psi-mi:“MI:0914”(association)0.350
NPKPNA6psi-mi:“MI:0914”(association)0.350

BioGRID (215): MRPS6 (Two-hybrid), MRPS6 (Affinity Capture-MS), MRPS6 (Affinity Capture-MS), MRPS18C (Co-fractionation), MRPS6 (Co-fractionation), MRPS6 (Affinity Capture-MS), MRPS6 (Affinity Capture-MS), MRPS6 (Affinity Capture-MS), MRPS6 (Affinity Capture-MS), MRPS6 (Affinity Capture-MS), MRPS6 (Affinity Capture-MS), MRPS6 (Affinity Capture-MS), MRPS6 (Affinity Capture-RNA), MRPS6 (Affinity Capture-MS), MRPS6 (Affinity Capture-MS)

ESM2 similar proteins: A4FUH0, A4FV08, A6QQL9, B5FWC0, D2K759, D2K760, D3K5L7, E1C6Q1, F1QH17, O22969, O94973, P16255, P35614, P35615, P46926, P50886, P50894, P58064, P62495, P62496, P62497, P62498, P82931, P82932, Q0VCK5, Q0VCX5, Q1RMS5, Q28IL6, Q3UA06, Q5R4C7, Q5R8T8, Q5R938, Q5U2Q7, Q5ZIJ2, Q5ZKQ6, Q64422, Q6P5R6, Q8BWY3, Q8CJ19, Q8LPJ4

Diamond homologs: P58064, P82931, P82932, Q5ZIJ2, Q9VZD5, Q7SB95, A8HVF1, P28778

SIGNOR signaling

1 interactions.

AEffectBMechanism
MRPS6“form complex”“28S mitochondrial small ribosomal subunit”binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 111 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 control2234.6×3e-26
Mitochondrial translation initiation2134.2×3e-25
Mitochondrial translation elongation2134.2×3e-25
Mitochondrial translation1933.5×1e-22
Mitochondrial translation termination2129.6×7e-24
Translation2015.9×3e-17
Mitochondrial protein degradation68.8×3e-03

GO biological processes:

GO termPartnersFoldFDR
mitochondrial translation2239.8×6e-27
translation1313.9×3e-09
protein phosphorylation85.7×1e-02

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 significance57
Likely benign2
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1460 predictions. Top by Δscore:

VariantEffectΔscore
21:34073742:GCGG:Gdonor_gain1.0000
21:34073744:GG:Gdonor_gain1.0000
21:34073745:GG:Gdonor_gain1.0000
21:34073745:GGT:Gdonor_loss1.0000
21:34073746:G:Cdonor_loss1.0000
21:34073746:G:GGdonor_gain1.0000
21:34073746:GTAA:Gdonor_loss1.0000
21:34073747:T:Gdonor_loss1.0000
21:34102909:G:GGdonor_gain1.0000
21:34117659:T:Gdonor_gain1.0000
21:34125321:A:AGacceptor_gain1.0000
21:34125322:A:Gacceptor_gain1.0000
21:34125327:A:AGacceptor_gain1.0000
21:34125328:C:Gacceptor_gain1.0000
21:34142402:TTGCA:Tacceptor_loss1.0000
21:34142405:CAG:Cacceptor_loss1.0000
21:34142406:A:AGacceptor_gain1.0000
21:34142406:A:ATacceptor_loss1.0000
21:34142407:G:Aacceptor_loss1.0000
21:34142407:G:GGacceptor_gain1.0000
21:34142407:GGT:Gacceptor_gain1.0000
21:34073741:AGCGG:Adonor_gain0.9900
21:34073742:GCGGG:Gdonor_gain0.9900
21:34073743:CGG:Cdonor_gain0.9900
21:34073744:GGG:Gdonor_gain0.9900
21:34125323:A:Gacceptor_gain0.9900
21:34125324:A:AGacceptor_gain0.9900
21:34125325:A:Gacceptor_gain0.9900
21:34125326:C:Gacceptor_gain0.9900
21:34125329:A:AGacceptor_gain0.9900

AlphaMissense

807 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
21:34073717:T:CL6P0.973
21:34125366:G:CR24P0.973
21:34142412:T:CF64L0.973
21:34142414:C:AF64L0.973
21:34142414:C:GF64L0.973
21:34142475:G:CD85H0.970
21:34125477:G:AG61D0.968
21:34125402:T:AV36E0.967
21:34125360:T:CL22S0.966
21:34142413:T:CF64S0.963
21:34142476:A:CD85A0.963
21:34142476:A:TD85V0.962
21:34142419:T:AV66E0.960
21:34125435:T:AL47H0.958
21:34142409:T:GY63D0.954
21:34142488:T:AI89N0.953
21:34073713:G:AE5K0.950
21:34125396:C:AA34E0.950
21:34125435:T:CL47P0.950
21:34142430:G:CA70P0.949
21:34125364:A:CK23N0.947
21:34125364:A:TK23N0.947
21:34125395:G:CA34P0.946
21:34125423:G:TG43V0.944
21:34142425:T:CF68S0.944
21:34073733:A:CK11N0.943
21:34073733:A:TK11N0.943
21:34125365:C:AR24S0.943
21:34142485:T:AV88E0.943
21:34125476:G:CG61R0.941

dbSNP variants (sampled 300 via entrez): RS1000064656 (21:34079990 T>C), RS1000090050 (21:34093571 A>G), RS1000156894 (21:34079854 T>G), RS1000190074 (21:34105135 G>A), RS1000196042 (21:34101557 C>G), RS1000204647 (21:34082853 T>A,C), RS1000282999 (21:34126893 G>A,T), RS1000299823 (21:34115620 C>T), RS1000362222 (21:34099044 A>C,G), RS1000373829 (21:34077518 A>G), RS1000517518 (21:34084485 A>G), RS1000566361 (21:34122531 G>A), RS1000637371 (21:34116753 A>G,T), RS1000651003 (21:34098717 A>ACTCTAACTTGACATGGCTTGGCACC), RS1000666878 (21:34116528 A>G)

Disease associations

OMIM: gene MIM:611973 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

5 associations (top):

StudyTraitp-value
GCST000340_3Myocardial infarction (early onset)6.000000e-11
GCST000998_26Coronary heart disease4.000000e-10
GCST003998_10Joint mobility (Beighton score)2.000000e-09
GCST011364_31Myocardial infarction7.000000e-12
GCST011365_35Myocardial infarction3.000000e-22

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0007905joint hypermobility measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Benzo(a)pyrenedecreases methylation, increases expression3
Acetaminophenaffects cotreatment, increases expression2
Air Pollutantsaffects cotreatment, increases abundance, increases oxidation, increases expression2
Valproic Aciddecreases methylation, increases expression, affects expression2
aristolochic acid Iincreases expression1
testosterone enanthateaffects expression1
triphenyl phosphateaffects expression1
alpha-pineneaffects cotreatment, increases oxidation, increases abundance1
bisphenol Aincreases expression1
testosterone undecanoatedecreases expression, affects cotreatment1
tris(2-butoxyethyl) phosphateaffects expression1
arseniteincreases methylation1
nickel chloridedecreases expression1
nickel sulfatedecreases expression1
methacrylaldehydeaffects cotreatment, increases oxidation, increases abundance1
beta-methylcholineaffects expression1
CGP 52608affects binding, increases reaction1
chloropicrinincreases expression1
deguelindecreases expression1
corosolic aciddecreases expression1
ICG 001decreases expression1
2-(1H-indazol-4-yl)-6-(4-methanesulfonylpiperazin-1-ylmethyl)-4-morpholin-4-ylthieno(3,2-d)pyrimidinedecreases expression, increases response to substance1
bisphenol Saffects cotreatment, decreases expression1
PCI 5002affects cotreatment, increases expression1
Resveratrolaffects cotreatment, increases expression1
Sunitinibincreases expression1
Acroleinaffects cotreatment, increases oxidation, increases abundance1
Atrazinedecreases expression1
Calcitriolincreases expression1
Cisplatinincreases 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): myocardial infarction