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MRPL54

gene
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Also known as mL54

Summary

MRPL54 (mitochondrial ribosomal protein L54, HGNC:16685) is a protein-coding gene on chromosome 19p13.3, encoding Large ribosomal subunit protein mL54 (Q6P161). It is a selective cancer dependency (DepMap: 35.8% 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.

Source: NCBI Gene 116541 — RefSeq curated summary.

At a glance

  • GWAS associations: 1
  • Clinical variants (ClinVar): 31 total — 1 pathogenic
  • Cancer dependency (DepMap): dependent in 35.8% of screened cell lines
  • MANE Select transcript: NM_172251

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:16685
Approved symbolMRPL54
Namemitochondrial ribosomal protein L54
Location19p13.3
Locus typegene with protein product
StatusApproved
AliasesmL54
Ensembl geneENSG00000183617
Ensembl biotypeprotein_coding
OMIM611858
Entrez116541

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 4 protein_coding

ENST00000330133, ENST00000589174, ENST00000884969, ENST00000939301

RefSeq mRNA: 1 — MANE Select: NM_172251 NM_172251

CCDS: CCDS12111

Canonical transcript exons

ENST00000330133 — 3 exons

ExonStartEnd
ENSE0000129198337626823762818
ENSE0000132596437672613767565
ENSE0000133019237651663765331

Expression profiles

Bgee: expression breadth ubiquitous, 246 present calls, max score 97.06.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 37.5237 / max 300.4404, expressed in 1822 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
17323936.70841822
1732400.8153456

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
granulocyteCL:000009497.06gold quality
right adrenal glandUBERON:000123396.39gold quality
right lobe of liverUBERON:000111496.32gold quality
right adrenal gland cortexUBERON:003582796.28gold quality
apex of heartUBERON:000209896.16gold quality
left adrenal glandUBERON:000123496.10gold quality
left adrenal gland cortexUBERON:003582595.86gold quality
adenohypophysisUBERON:000219695.84gold quality
mucosa of transverse colonUBERON:000499195.77gold quality
monocyteCL:000057695.66gold quality
leukocyteCL:000073895.63gold quality
body of stomachUBERON:000116195.57gold quality
olfactory segment of nasal mucosaUBERON:000538695.49gold quality
body of pancreasUBERON:000115095.31gold quality
adrenal cortexUBERON:000123595.25gold quality
pituitary glandUBERON:000000795.00gold quality
left coronary arteryUBERON:000162694.80gold quality
adrenal glandUBERON:000236994.66gold quality
Brodmann (1909) area 9UBERON:001354094.62gold quality
esophagogastric junction muscularis propriaUBERON:003584194.62gold quality
right atrium auricular regionUBERON:000663194.61gold quality
heart left ventricleUBERON:000208494.51gold quality
coronary arteryUBERON:000162194.47gold quality
left lobe of thyroid glandUBERON:000112094.40gold quality
lower esophagus muscularis layerUBERON:003583394.40gold quality
lower esophagusUBERON:001347394.39gold quality
right coronary arteryUBERON:000162594.35gold quality
adult mammalian kidneyUBERON:000008294.34gold quality
C1 segment of cervical spinal cordUBERON:000646994.29gold quality
cardiac ventricleUBERON:000208294.28gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes13.87

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

3 targeting MRPL54, 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-444799.8567.812900
HSA-MIR-1912-3P99.3267.40936
HSA-MIR-1295B-5P99.0367.50810

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 35.8% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 1)

  • Expression analysis of mammalian mitochondrial ribosomal protein genes (PMID:32987154)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriomrpl54ENSDARG00000071468
mus_musculusMrpl54ENSMUSG00000034932
rattus_norvegicusMrpl54ENSRNOG00000020464
drosophila_melanogastermRpL54FBGN0034579
caenorhabditis_elegansmrpl-54WBGENE00009128

Protein

Protein identifiers

Large ribosomal subunit protein mL54 — Q6P161 (reviewed: Q6P161)

Alternative names: 39S ribosomal protein L54, mitochondrial

All UniProt accessions (2): K7ENN2, Q6P161

UniProt curated annotations — full annotation on UniProt →

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.

Subcellular location. Mitochondrion.

Similarity. Belongs to the mitochondrion-specific ribosomal protein mL54 family.

RefSeq proteins (1): NP_758455* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR013870Ribosomal_mL54Family

Pfam: PF08561

UniProt features (4 total): transit peptide 1, chain 1, helix 1, turn 1

Structure

Experimental structures (PDB)

78 structures, top 30 by resolution.

PDBMethodResolution (Å)
7QI4ELECTRON MICROSCOPY2.21
8RRIELECTRON MICROSCOPY2.4
8QU5ELECTRON MICROSCOPY2.42
9OLFELECTRON MICROSCOPY2.46
7PO4ELECTRON MICROSCOPY2.56
6ZM6ELECTRON MICROSCOPY2.59
7O9MELECTRON MICROSCOPY2.6
7OF6ELECTRON MICROSCOPY2.6
9CN3ELECTRON MICROSCOPY2.62
7QI5ELECTRON MICROSCOPY2.63
7OF2ELECTRON MICROSCOPY2.7
7OF4ELECTRON MICROSCOPY2.7
9PR4ELECTRON MICROSCOPY2.77
9PRAELECTRON MICROSCOPY2.83
8ANYELECTRON MICROSCOPY2.85
6ZM5ELECTRON MICROSCOPY2.89
7ODRELECTRON 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
8QSJELECTRON MICROSCOPY3
9UWHELECTRON MICROSCOPY3
9PGIELECTRON MICROSCOPY3.02
5OOMELECTRON MICROSCOPY3.03
8PK0ELECTRON MICROSCOPY3.03

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q6P161-F174.730.35

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: 113 (showing top): GOBP_MITOCHONDRIAL_TRANSLATION, GOBP_TRANSLATION, GOMF_STRUCTURAL_CONSTITUENT_OF_RIBOSOME, INGRAM_SHH_TARGETS_DN, GOCC_MITOCHONDRIAL_ENVELOPE, ELK1_01, GOCC_LARGE_RIBOSOMAL_SUBUNIT, GOCC_RIBOSOME, GOCC_ORGANELLAR_RIBOSOME, GOCC_MITOCHONDRIAL_MATRIX, GOCC_ORGANELLE_INNER_MEMBRANE, GOCC_RIBOSOMAL_SUBUNIT, GOCC_RIBONUCLEOPROTEIN_COMPLEX, GOCC_MITOCHONDRIAL_PROTEIN_CONTAINING_COMPLEX, chr19p13

GO Biological Process (1): 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), 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
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
intracellular membraneless organelle1
protein-containing complex1

Protein interactions and networks

STRING

1576 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
MRPL54MRPL46Q9H2W6585
MRPL54MRPS22P82650578
MRPL54MRPL1Q9BYD6547
MRPL54MRPL52Q86TS9536
MRPL54RBFAQ8N0V3496
MRPL54MRPL47Q9HD33486
MRPL54MRPS33Q9Y291475
MRPL54TNRC18O15417474
MRPL54MRPL42Q9Y6G3474
MRPL54MRPL41Q8IXM3468
MRPL54OSBPL6Q9BZF3465
MRPL54MRPS18BQ9Y676449
MRPL54MRPL33O75394448
MRPL54DNPEPQ9ULA0447
MRPL54GALNT18Q6P9A2443

IntAct

34 interactions, top by confidence:

ABTypeScore
NDUFS3NDUFS8psi-mi:“MI:0914”(association)0.730
MRPL11MRPL54psi-mi:“MI:0915”(physical association)0.560
MRPL54MRPL11psi-mi:“MI:0915”(physical association)0.560
MRPL13GTPBP10psi-mi:“MI:0914”(association)0.530
MRPL18GTPBP10psi-mi:“MI:0914”(association)0.530
MRPL2GTPBP10psi-mi:“MI:0914”(association)0.530
NDUFAB1MIEF1psi-mi:“MI:0915”(physical association)0.490
MRPL54psi-mi:“MI:0915”(physical association)0.400
PcnaSIVA1psi-mi:“MI:0914”(association)0.350
B4galt1SLC35B1psi-mi:“MI:0914”(association)0.350
VPS16IPO7psi-mi:“MI:0914”(association)0.350
MRPL50MRPL43psi-mi:“MI:0914”(association)0.350
MRPL9MRPL43psi-mi:“MI:0914”(association)0.350
CENPAATP5PDpsi-mi:“MI:0914”(association)0.350
MKI67ARHGAP10psi-mi:“MI:0914”(association)0.350
psi-mi:“MI:0914”(association)0.350
MTRES1ALDH1L1psi-mi:“MI:0914”(association)0.350
NPOLRMTpsi-mi:“MI:0914”(association)0.350
LIN28AMEX3Apsi-mi:“MI:0914”(association)0.350
MRPL42UBA6psi-mi:“MI:0914”(association)0.350
NEIL1GTPBP10psi-mi:“MI:0914”(association)0.350
MRPS30psi-mi:“MI:0914”(association)0.350
MRPL27psi-mi:“MI:0914”(association)0.350
MRPL53psi-mi:“MI:0914”(association)0.350
MRPL30psi-mi:“MI:0914”(association)0.350
GADD45GIP1psi-mi:“MI:0914”(association)0.350
MRPL12psi-mi:“MI:0914”(association)0.350
MRPL12GTPBP10psi-mi:“MI:0914”(association)0.350
MRPL42GTPBP10psi-mi:“MI:0914”(association)0.350

BioGRID (70): MRPL54 (Co-fractionation), MRPL54 (Affinity Capture-MS), MRPL54 (Affinity Capture-MS), MRPL54 (Affinity Capture-MS), MRPL54 (Affinity Capture-MS), MRPL54 (Affinity Capture-MS), MRPL54 (Affinity Capture-MS), MRPL54 (Affinity Capture-MS), MRPL54 (Affinity Capture-MS), MRPL54 (Affinity Capture-MS), MRPL54 (Affinity Capture-MS), MRPL54 (Affinity Capture-MS), MRPL54 (Affinity Capture-MS), MRPL54 (Affinity Capture-MS), MRPL54 (Affinity Capture-MS)

ESM2 similar proteins: O09111, P0C2B7, P0C2B8, P0C2B9, P25712, P56181, P82649, P82913, P82927, P83565, Q0MQJ0, Q0MQJ1, Q0MQJ2, Q0MQJ3, Q0MQJ4, Q0MQJ5, Q2TBI6, Q3MHJ5, Q3T040, Q5EA71, Q5I0K8, Q5R4S3, Q5R504, Q5TC12, Q5TM62, Q6DDY9, Q6DQX6, Q6P161, Q7Z7F7, Q80X85, Q811I0, Q86TS9, Q8BK30, Q8HXG5, Q99N84, Q9BYC8, Q9CPV3, Q9CPW3, Q9CQ40, Q9CZ83

Diamond homologs: Q1LXI5, Q3MHJ5, Q6P161, Q9CPW3

SIGNOR signaling

1 interactions.

AEffectBMechanism
MRPL54“form complex”“39S mitochondrial large ribosomal subunit”binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 40 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 control1871.3×1e-28
Mitochondrial translation initiation1561.4×1e-22
Mitochondrial translation elongation1561.4×1e-22
Mitochondrial translation1357.7×3e-19
Mitochondrial translation termination1553.1×9e-22
Translation1326.0×1e-14

GO biological processes:

GO termPartnersFoldFDR
mitochondrial translation1574.5×3e-23
translation823.5×8e-08

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic1
Likely pathogenic0
Uncertain significance27
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (1)

Variant IDHGVSClassification
1037962NC_000019.9:g.(?3762699)(3808981_?)delPathogenic

SpliceAI

258 predictions. Top by Δscore:

VariantEffectΔscore
19:3762817:AGG:Adonor_loss1.0000
19:3762819:GTGA:Gdonor_loss1.0000
19:3765155:C:Aacceptor_gain1.0000
19:3765160:CCCCA:Cacceptor_gain1.0000
19:3765161:CCCA:Cacceptor_gain1.0000
19:3765162:CCA:Cacceptor_gain1.0000
19:3765163:CAG:Cacceptor_gain1.0000
19:3765164:A:ACacceptor_gain1.0000
19:3765164:A:AGacceptor_gain1.0000
19:3765165:G:Cacceptor_gain1.0000
19:3765165:G:GCacceptor_gain1.0000
19:3765165:GT:Gacceptor_gain1.0000
19:3765165:GTT:Gacceptor_gain1.0000
19:3765165:GTTA:Gacceptor_gain1.0000
19:3765165:GTTAT:Gacceptor_gain1.0000
19:3765285:G:GTdonor_gain1.0000
19:3765294:G:GTdonor_gain1.0000
19:3765312:GATGC:Gdonor_gain1.0000
19:3765316:C:Gdonor_gain1.0000
19:3765327:GAATG:Gdonor_gain1.0000
19:3765328:AATG:Adonor_gain1.0000
19:3765329:ATG:Adonor_gain1.0000
19:3765330:TG:Tdonor_gain1.0000
19:3765331:GG:Gdonor_gain1.0000
19:3765332:G:GGdonor_gain1.0000
19:3765332:G:Tdonor_loss1.0000
19:3765333:T:Adonor_loss1.0000
19:3762819:G:GGdonor_gain0.9900
19:3765336:G:GGdonor_gain0.9900
19:3767250:A:AGacceptor_gain0.9900

AlphaMissense

887 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
19:3765330:T:AW95R0.989
19:3765330:T:CW95R0.989
19:3765262:C:AA72D0.987
19:3767265:T:CF97L0.985
19:3767267:C:AF97L0.985
19:3767267:C:GF97L0.985
19:3765321:T:CY92H0.983
19:3767341:G:CR122P0.983
19:3767261:G:CW95C0.982
19:3767261:G:TW95C0.982
19:3767359:G:CR128P0.978
19:3767345:A:CK123N0.977
19:3767345:A:TK123N0.977
19:3767332:G:CR119P0.975
19:3765275:C:AN76K0.972
19:3765275:C:GN76K0.972
19:3765267:G:CG74R0.969
19:3765322:A:CY92S0.969
19:3765322:A:GY92C0.967
19:3767330:G:CW118C0.966
19:3767330:G:TW118C0.966
19:3767338:T:CL121P0.965
19:3765321:T:GY92D0.964
19:3767326:A:CY117S0.964
19:3767325:T:CY117H0.963
19:3765250:T:CL68P0.960
19:3765250:T:AL68H0.958
19:3767368:G:CR131P0.958
19:3767326:A:GY117C0.957
19:3767263:T:AL96Q0.955

dbSNP variants (sampled 300 via entrez): RS1000215475 (19:3767032 G>A,C), RS1000501604 (19:3765162 C>A,G,T), RS1000565899 (19:3766782 C>T), RS1000956396 (19:3768017 C>T), RS1001169222 (19:3765553 C>T), RS1001562234 (19:3766482 G>A), RS1001657406 (19:3761753 CG>C), RS1001996028 (19:3761784 G>A,C,T), RS1002707242 (19:3762861 C>G,T), RS1003556815 (19:3764379 G>A,T), RS1003725861 (19:3764232 A>C,G), RS1004337171 (19:3761879 T>C), RS1004562357 (19:3763426 T>C), RS1004673972 (19:3763123 A>C), RS1005228571 (19:3760939 A>C)

Disease associations

OMIM: gene MIM:611858 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

StudyTraitp-value
GCST007637_40Diffusing capacity of carbon monoxide6.000000e-06

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0009369diffusing capacity of the lung for carbon monoxide

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

25 total (human), top 25 by PubMed support.

ChemicalActions (top 5)PubMed papers
Acetaminophenaffects cotreatment, decreases expression2
Smokeincreases abundance, increases expression, decreases expression2
Cyclosporinedecreases methylation, increases expression2
triphenyl phosphateaffects expression1
bisphenol Adecreases expression1
beta-methylcholineaffects expression1
perfluorooctane sulfonic acidincreases expression1
monomethylarsonous aciddecreases expression1
abrineincreases expression1
bisphenol Sdecreases expression1
(+)-JQ1 compounddecreases expression1
Air Pollutantsincreases abundance, increases expression1
Benzo(a)pyrenedecreases expression1
Cannabidiolincreases expression1
Coalincreases expression, increases abundance1
Diethylhexyl Phthalatedecreases expression1
Diurondecreases expression1
Ethyl Methanesulfonatedecreases expression1
Lipopolysaccharidesaffects cotreatment, decreases expression1
Rotenoneincreases expression1
Selenomethionineaffects expression1
Dronabinoldecreases expression1
Valproic Aciddecreases expression, increases methylation1
Aflatoxin B1decreases methylation1
Lactic Aciddecreases 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.

About this page

Generated deterministically by Sugi Atlas from primary biomedical databases via BioBTree. Every record on this page traces to a primary source.

Generated
Atlas version
v1.1.4
BioBTree
v2.0.2

Sources 75

This page pulls from 75 datasets indexed by BioBTree:

alphafoldalphamissenseantibodybgeebgee_evidencebindingdbbiogrid_interactionbrendabrenda_kineticsccdscellosauruschembl_activitychembl_targetciviccivic_evidenceclingen_dosageclingen_gene_validityclinical_trialsclinvarcollectrictd_gene_interactiondbsnpdepmapdiamond_similarityefoensemblentrezesm2_similarityexonfantom5_genefantom5_promotergenccgenerifgogoparentgtopdbgwasgwas_studyhgnchpointactinterprointogenjasparmeshmimmirdbmondomsigdborphanetorthologparalogpdbpfampharmgkb_clinicalpharmgkb_genepharmgkb_guidelinepharmgkb_variantpubchempubchem_activitypubchem_assaypubmedreactomereactomeparentrefseqrhearnacentralscxa_expressionscxa_gene_experimentsignorspliceaistring_interactiontranscriptufeatureuniprot