MRPL55

gene
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Also known as bL31m

Summary

MRPL55 (mitochondrial ribosomal protein L55, HGNC:16686) is a protein-coding gene on chromosome 1q42.13, encoding Large ribosomal subunit protein mL55 (Q7Z7F7). It is a selective cancer dependency (DepMap: 64.7% 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 39S subunit protein. Multiple transcript variants encoding two different isoforms were identified through sequence analysis.

Source: NCBI Gene 128308 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 38 total
  • Cancer dependency (DepMap): dependent in 64.7% of screened cell lines
  • MANE Select transcript: NM_181463

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:16686
Approved symbolMRPL55
Namemitochondrial ribosomal protein L55
Location1q42.13
Locus typegene with protein product
StatusApproved
AliasesbL31m
Ensembl geneENSG00000162910
Ensembl biotypeprotein_coding
OMIM611859
Entrez128308

Gene structure

Transcript identifiers

Ensembl transcripts: 123 — 115 protein_coding, 5 retained_intron, 3 protein_coding_CDS_not_defined

ENST00000295008, ENST00000336300, ENST00000336520, ENST00000348259, ENST00000366731, ENST00000366732, ENST00000366733, ENST00000366734, ENST00000366735, ENST00000366736, ENST00000366738, ENST00000366739, ENST00000366740, ENST00000366741, ENST00000366742, ENST00000366744, ENST00000366746, ENST00000366747, ENST00000391867, ENST00000411464, ENST00000430433, ENST00000457264, ENST00000459783, ENST00000464148, ENST00000465268, ENST00000473066, ENST00000475832, ENST00000476267, ENST00000483159, ENST00000489430, ENST00000492170, ENST00000495434, ENST00000495899, ENST00000497758, ENST00000877018, ENST00000877019, ENST00000877020, ENST00000877021, ENST00000877022, ENST00000877023, ENST00000877024, ENST00000877025, ENST00000877026, ENST00000877027, ENST00000877028, ENST00000877029, ENST00000877030, ENST00000877031, ENST00000877032, ENST00000877033, ENST00000877034, ENST00000877035, ENST00000877036, ENST00000877037, ENST00000877038, ENST00000877039, ENST00000877040, ENST00000877041, ENST00000877042, ENST00000877043, ENST00000877044, ENST00000877045, ENST00000877046, ENST00000877047, ENST00000877048, ENST00000877049, ENST00000877050, ENST00000877051, ENST00000877052, ENST00000877053, ENST00000877054, ENST00000877055, ENST00000877056, ENST00000877057, ENST00000927937, ENST00000927938, ENST00000927939, ENST00000927940, ENST00000927941, ENST00000927942, ENST00000927943, ENST00000927944, ENST00000927945, ENST00000927946, ENST00000927947, ENST00000927948, ENST00000927949, ENST00000927950, ENST00000927951, ENST00000927952, ENST00000927953, ENST00000927954, ENST00000927955, ENST00000927956, ENST00000927957, ENST00000927958, ENST00000927959, ENST00000927960, ENST00000927961, ENST00000927962, ENST00000927963, ENST00000927964, ENST00000927965, ENST00000927966, ENST00000927967, ENST00000927968, ENST00000927969, ENST00000927970, ENST00000927971, ENST00000927972, ENST00000927973, ENST00000927974, ENST00000927975, ENST00000927976, ENST00000927977, ENST00000927978, ENST00000927979, ENST00000927980, ENST00000927981, ENST00000927982, ENST00000957205, ENST00000957206, ENST00000957207

RefSeq mRNA: 9 — MANE Select: NM_181463 NM_001321284, NM_181441, NM_181454, NM_181455, NM_181456, NM_181462, NM_181463, NM_181464, NM_181465

CCDS: CCDS1567, CCDS44325

Canonical transcript exons

ENST00000336520 — 5 exons

ExonStartEnd
ENSE00001337183228108955228109021
ENSE00001897589228109149228109299
ENSE00003556550228107668228107869
ENSE00003680201228108235228108318
ENSE00003841621228106685228106918

Expression profiles

Bgee: expression breadth ubiquitous, 234 present calls, max score 96.89.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 40.8619 / max 256.1624, expressed in 1820 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
1781739.23291820
178161.2775833
178150.3516157

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
apex of heartUBERON:000209896.89gold quality
prefrontal cortexUBERON:000045196.41gold quality
right lobe of liverUBERON:000111496.30gold quality
Brodmann (1909) area 9UBERON:001354096.07gold quality
anterior cingulate cortexUBERON:000983595.84gold quality
olfactory segment of nasal mucosaUBERON:000538695.71gold quality
hindlimb stylopod muscleUBERON:000425295.68gold quality
adenohypophysisUBERON:000219695.67gold quality
right adrenal glandUBERON:000123395.60gold quality
left adrenal gland cortexUBERON:003582595.53gold quality
right adrenal gland cortexUBERON:003582795.53gold quality
right frontal lobeUBERON:000281095.38gold quality
left adrenal glandUBERON:000123495.30gold quality
esophagogastric junction muscularis propriaUBERON:003584195.02gold quality
amygdalaUBERON:000187694.89gold quality
hypothalamusUBERON:000189894.82gold quality
muscle layer of sigmoid colonUBERON:003580594.75gold quality
body of stomachUBERON:000116194.74gold quality
adrenal cortexUBERON:000123594.72gold quality
C1 segment of cervical spinal cordUBERON:000646994.72gold quality
lower esophagus muscularis layerUBERON:003583394.71gold quality
lower esophagusUBERON:001347394.70gold quality
putamenUBERON:000187494.69gold quality
nucleus accumbensUBERON:000188294.61gold quality
metanephros cortexUBERON:001053394.48gold quality
left coronary arteryUBERON:000162694.41gold quality
left lobe of thyroid glandUBERON:000112094.37gold quality
endocervixUBERON:000045894.31gold quality
right lobe of thyroid glandUBERON:000111994.30gold quality
right atrium auricular regionUBERON:000663194.30gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-GEOD-75367no416.70
E-ANND-3no0.00

Regulation

Is transcription factor: no

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 64.7% of screened cell lines.

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
mus_musculusMrpl55ENSMUSG00000036860
rattus_norvegicusMrpl55ENSRNOG00000002943

Protein

Protein identifiers

Large ribosomal subunit protein mL55Q7Z7F7 (reviewed: Q7Z7F7)

Alternative names: 39S ribosomal protein L55, mitochondrial, Mitochondrial large ribosomal subunit protein bL31m

All UniProt accessions (6): A0A087X2A2, A0A0A0MST4, A0A0G2JMK5, Q7Z7F7, X6R631, X6RIW1

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 mL55 family.

Isoforms (2)

UniProt IDNamesCanonical?
Q7Z7F7-11yes
Q7Z7F7-22

RefSeq proteins (9): NP_001308213, NP_852106, NP_852119, NP_852120, NP_852121, NP_852127, NP_852128, NP_852129, NP_852130 (=MANE)

Domains & families (InterPro)

IDNameType
IPR018615Ribosomal_mL55Family
IPR044884Ribosomal_mL55_sfHomologous_superfamily

Pfam: PF09776

UniProt features (11 total): strand 4, sequence variant 2, transit peptide 1, chain 1, modified residue 1, splice variant 1, helix 1

Structure

Experimental structures (PDB)

82 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
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
8OISELECTRON MICROSCOPY3

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q7Z7F7-F179.800.38

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): 85

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: 87 (showing top): STARK_PREFRONTAL_CORTEX_22Q11_DELETION_DN, GOBP_MITOCHONDRIAL_TRANSLATION, GOBP_TRANSLATION, GOMF_STRUCTURAL_CONSTITUENT_OF_RIBOSOME, GOCC_MITOCHONDRIAL_ENVELOPE, 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, GOMF_STRUCTURAL_MOLECULE_ACTIVITY, GOCC_ORGANELLE_ENVELOPE

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

GO Molecular Function (1): structural constituent of ribosome (GO:0003735)

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
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
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

1488 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
MRPL55MRPL52Q86TS9721
MRPL55MRPS30Q9NP92644
MRPL55MRPL51Q4U2R6614
MRPL55MRPS14O60783577
MRPL55RPL6Q02878555
MRPL55RPL26P61254522
MRPL55MRPS25P82663510
MRPL55MRPL43Q8N983484
MRPL55SYF2O95926480
MRPL55MRPS21P82921478
MRPL55BEAN1Q3B7T3475
MRPL55COMMD5Q9GZQ3469
MRPL55LDHDQ86WU2464
MRPL55CCNDBP1O95273455
MRPL55MRPS15P82914452

IntAct

111 interactions, top by confidence:

ABTypeScore
PLK1EVI5psi-mi:“MI:0914”(association)0.660
MRPS30GTPBP10psi-mi:“MI:0914”(association)0.640
LIN28AIGF2BP3psi-mi:“MI:0914”(association)0.640
NPKPNA6psi-mi:“MI:0914”(association)0.550
MRPL50GTPBP10psi-mi:“MI:0914”(association)0.530
MRPL2GTPBP10psi-mi:“MI:0914”(association)0.530
MRPL46MRPL55psi-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
NDUFAB1MIEF1psi-mi:“MI:0915”(physical association)0.490
Cdca5ATP5MF-PTCD1psi-mi:“MI:0914”(association)0.350
CHORDC1SSR3psi-mi:“MI:0914”(association)0.350
PARD6BPARD3psi-mi:“MI:0914”(association)0.350
Cdc26psi-mi:“MI:0914”(association)0.350
Rab5cpsi-mi:“MI:0914”(association)0.350
MYO1CPLEKHG3psi-mi:“MI:0914”(association)0.350
RAB5Cpsi-mi:“MI:0914”(association)0.350
CBX4SDC2psi-mi:“MI:0914”(association)0.350
Cdkn2aipSF1psi-mi:“MI:0914”(association)0.350
UGGT1SF3B1psi-mi:“MI:0914”(association)0.350
HNRNPDARHGAP32psi-mi:“MI:0914”(association)0.350
BAG6CNOT1psi-mi:“MI:0914”(association)0.350
SORT1SH3PXD2Bpsi-mi:“MI:0914”(association)0.350

BioGRID (172): MRPL55 (Affinity Capture-MS), MRPL55 (Affinity Capture-MS), MRPL55 (Affinity Capture-MS), MRPL55 (Affinity Capture-MS), MRPL55 (Affinity Capture-MS), MRPL55 (Affinity Capture-MS), MRPL55 (Affinity Capture-MS), MRPL55 (Affinity Capture-MS), MRPL55 (Affinity Capture-MS), MRPL55 (Affinity Capture-MS), MRPL55 (Co-fractionation), MRPL55 (Co-fractionation), MRPL55 (Co-fractionation), MRPL55 (Affinity Capture-MS), MRPL55 (Affinity Capture-MS)

ESM2 similar proteins: A1A4P4, M0R3K6, O09111, P0C2B7, P0C2B8, P0C2B9, P56181, P82649, P82927, P83565, Q08DT6, Q0MQJ0, Q0MQJ1, Q0MQJ2, Q0MQJ3, Q0MQJ4, Q0MQJ5, Q1ECT8, Q290P4, Q3SZ86, Q4G0I0, Q4V7Q1, Q5R4S3, Q5RFR4, Q5TC12, Q5XIC2, Q5XJW2, Q6DQX6, Q7Z7F7, Q80ZS3, Q811I0, Q86TS9, Q8HXG5, Q8K2Y7, Q8SPE7, Q8TAE8, Q9BYN8, Q9C086, Q9CPV3, Q9CR59

Diamond homologs: P0C2B8, Q7Z7F7, Q9CZ83, Q9VE04

SIGNOR signaling

1 interactions.

AEffectBMechanism
MRPL55“form complex”“39S mitochondrial large ribosomal subunit”binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 98 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 control2946.9×4e-40
Mitochondrial translation2443.5×2e-32
Mitochondrial translation initiation2643.4×4e-35
Mitochondrial translation elongation2643.4×4e-35
Mitochondrial translation termination2637.6×2e-33
Translation2621.2×2e-26
Peptide chain elongation1016.7×1e-08
Viral mRNA Translation1016.7×1e-08

GO biological processes:

GO termPartnersFoldFDR
mitochondrial translation2854.7×1e-39
translation2427.7×4e-26
cytoplasmic translation1020.8×7e-09
negative regulation of translation715.4×4e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance28
Likely benign1
Benign1

Top pathogenic / likely-pathogenic (0)

SpliceAI

396 predictions. Top by Δscore:

VariantEffectΔscore
1:228106914:GGCAT:Gacceptor_gain1.0000
1:228106915:GCAT:Gacceptor_gain1.0000
1:228106916:CATC:Cacceptor_gain1.0000
1:228106919:C:CCacceptor_gain1.0000
1:228106919:CTG:Cacceptor_loss1.0000
1:228107661:AGCTT:Adonor_loss1.0000
1:228107663:CTTA:Cdonor_loss1.0000
1:228107665:TACCG:Tdonor_loss1.0000
1:228107666:A:ACdonor_gain1.0000
1:228107666:ACCG:Adonor_gain1.0000
1:228107667:C:Adonor_loss1.0000
1:228107667:C:CCdonor_gain1.0000
1:228107667:CCG:Cdonor_gain1.0000
1:228107667:CCGC:Cdonor_gain1.0000
1:228106916:CAT:Cacceptor_gain0.9900
1:228106917:AT:Aacceptor_gain0.9900
1:228107662:GCTT:Gdonor_gain0.9900
1:228107664:TTA:Tdonor_gain0.9900
1:228107665:T:TCdonor_gain0.9900
1:228107666:A:Gdonor_gain0.9900
1:228107666:ACCGC:Adonor_gain0.9900
1:228107667:C:Tdonor_gain0.9900
1:228107667:CCGCC:Cdonor_gain0.9900
1:228107688:C:CAdonor_gain0.9900
1:228107866:CCGG:Cacceptor_gain0.9900
1:228107867:CGG:Cacceptor_gain0.9900
1:228107867:CGGC:Cacceptor_gain0.9900
1:228107870:C:CCacceptor_gain0.9900
1:228106915:GCATC:Gacceptor_gain0.9800
1:228106916:CATCT:Cacceptor_gain0.9800

AlphaMissense

809 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
1:228107742:A:CY52D0.907
1:228107712:A:GS62P0.903
1:228106881:C:GR89P0.875
1:228107714:C:AG61V0.870
1:228107699:A:TI66N0.865
1:228107684:G:TP71Q0.840
1:228106781:G:CF122L0.834
1:228106781:G:TF122L0.834
1:228106783:A:GF122L0.834
1:228107716:A:CD60E0.827
1:228107716:A:TD60E0.827
1:228107685:G:AP71S0.825
1:228107791:G:CS35R0.821
1:228107791:G:TS35R0.821
1:228107793:T:GS35R0.821
1:228107681:C:GR72P0.805
1:228107742:A:TY52N0.805
1:228107699:A:CI66S0.797
1:228107694:A:CY68D0.795
1:228107718:C:GD60H0.789
1:228107763:G:TR45S0.784
1:228107741:T:GY52S0.781
1:228107714:C:TG61D0.780
1:228107735:A:TV54E0.774
1:228107699:A:GI66T0.769
1:228107685:G:TP71T0.763
1:228107717:T:AD60V0.763
1:228106882:G:TR89S0.762
1:228106778:C:AW123C0.758
1:228106778:C:GW123C0.758

dbSNP variants (sampled 300 via entrez): RS1000496843 (1:228109242 A>G), RS1001112946 (1:228107406 A>C), RS1001754115 (1:228110706 G>A), RS1002092502 (1:228109099 G>C), RS1003887443 (1:228109274 G>A,C,T), RS1004001876 (1:228109453 C>CG), RS1004181897 (1:228108389 C>T), RS1004515162 (1:228107282 G>A,C), RS1004896319 (1:228110552 A>G), RS1007243767 (1:228106790 G>A), RS1007857087 (1:228109873 G>C), RS1008475603 (1:228109443 G>A), RS1008817384 (1:228108120 A>G), RS1009369409 (1:228109406 G>T), RS1009730022 (1:228109203 C>T)

Disease associations

OMIM: gene MIM:611859 | 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

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

ChemicalActions (top 5)PubMed papers
Benzo(a)pyrenedecreases expression, decreases methylation3
triphenyl phosphateaffects expression1
bisphenol Adecreases expression1
beta-lapachoneincreases expression1
arseniteincreases reaction, affects binding1
sodium arseniteincreases abundance, increases expression1
perfluorooctane sulfonic acidincreases expression1
CGP 52608affects binding, increases reaction1
2-palmitoylglycerolincreases expression1
ICG 001decreases expression1
jinfukangincreases expression1
Acetaminophenincreases expression1
Ethanolaffects cotreatment, increases abundance, increases expression1
Arsenicincreases abundance, increases expression1
Dietary Carbohydratesdecreases expression1
Diethylstilbestroldecreases expression1
Doxorubicinincreases expression1
Gasolineaffects cotreatment, increases abundance, increases expression1
Hydrogen Peroxideaffects expression1
Polycyclic Aromatic Hydrocarbonsaffects cotreatment, increases abundance, increases expression1
Smokedecreases expression1
Thiramdecreases expression1
Urethanedecreases expression1
Asbestos, Crocidoliteincreases expression1
Particulate Matteraffects cotreatment, increases abundance, increases 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.