MRPL48

gene
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Also known as CGI-118mL48

Summary

MRPL48 (mitochondrial ribosomal protein L48, HGNC:16653) is a protein-coding gene on chromosome 11q13.4, encoding Large ribosomal subunit protein mL48 (Q96GC5). It is a selective cancer dependency (DepMap: 15.1% 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. A pseudogene corresponding to this gene is found on chromosome 6p. Several transcript variants, some protein-coding and some non-protein coding, have been found for this gene.

Source: NCBI Gene 51642 — RefSeq curated summary.

At a glance

  • GWAS associations: 3
  • Clinical variants (ClinVar): 40 total
  • Cancer dependency (DepMap): dependent in 15.1% of screened cell lines
  • MANE Select transcript: NM_016055

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:16653
Approved symbolMRPL48
Namemitochondrial ribosomal protein L48
Location11q13.4
Locus typegene with protein product
StatusApproved
AliasesCGI-118, mL48
Ensembl geneENSG00000175581
Ensembl biotypeprotein_coding
OMIM611853
Entrez51642

Gene structure

Transcript identifiers

Ensembl transcripts: 17 — 11 protein_coding, 5 nonsense_mediated_decay, 1 retained_intron

ENST00000310614, ENST00000314282, ENST00000398483, ENST00000411840, ENST00000497094, ENST00000508278, ENST00000535277, ENST00000537007, ENST00000540162, ENST00000542303, ENST00000543058, ENST00000543374, ENST00000544140, ENST00000544819, ENST00000889271, ENST00000930868, ENST00000930869

RefSeq mRNA: 4 — MANE Select: NM_016055 NM_001318498, NM_001318499, NM_001318500, NM_016055

CCDS: CCDS44676, CCDS81594

Canonical transcript exons

ENST00000310614 — 8 exons

ExonStartEnd
ENSE000023046307386429673865133
ENSE000023088237378787473787992
ENSE000035375457380831373808350
ENSE000035414777380502773805079
ENSE000035620037382570873825796
ENSE000035913577384480773844976
ENSE000036007627386317273863261
ENSE000036712037385990773860009

Expression profiles

Bgee: expression breadth ubiquitous, 287 present calls, max score 95.79.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 29.0974 / max 354.5567, expressed in 1809 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
11582828.55471809
1158290.5426314

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
C1 segment of cervical spinal cordUBERON:000646995.79gold quality
spinal cordUBERON:000224094.73gold quality
hindlimb stylopod muscleUBERON:000425294.46gold quality
mucosa of transverse colonUBERON:000499194.46gold quality
ganglionic eminenceUBERON:000402394.30gold quality
cortical plateUBERON:000534394.14gold quality
corpus callosumUBERON:000233693.75gold quality
ponsUBERON:000098893.73gold quality
prefrontal cortexUBERON:000045193.65gold quality
cerebellar cortexUBERON:000212992.88gold quality
cerebellar hemisphereUBERON:000224592.86gold quality
putamenUBERON:000187492.57gold quality
right hemisphere of cerebellumUBERON:001489092.36gold quality
islet of LangerhansUBERON:000000692.21gold quality
caudate nucleusUBERON:000187392.20gold quality
nucleus accumbensUBERON:000188292.16gold quality
ventricular zoneUBERON:000305392.15gold quality
anterior cingulate cortexUBERON:000983592.08gold quality
cingulate cortexUBERON:000302792.00gold quality
amygdalaUBERON:000187691.97gold quality
inferior vagus X ganglionUBERON:000536391.96gold quality
cerebellumUBERON:000203791.95gold quality
granulocyteCL:000009491.87gold quality
right frontal lobeUBERON:000281091.85gold quality
body of pancreasUBERON:000115091.56gold quality
Brodmann (1909) area 9UBERON:001354091.50gold quality
rectumUBERON:000105291.48gold quality
apex of heartUBERON:000209891.46gold quality
hypothalamusUBERON:000189891.41gold quality
right adrenal glandUBERON:000123391.39gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes6.59
E-MTAB-7606no394.22
E-MTAB-6058no183.55
E-CURD-112no2.62

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

10 targeting MRPL48, 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-118499.9968.191458
HSA-MIR-96-5P99.9572.802140
HSA-MIR-5004-5P99.6866.631294
HSA-MIR-10394-5P99.6566.831852
HSA-MIR-120599.6566.761826
HSA-MIR-942-5P99.4168.401977
HSA-MIR-4777-3P99.1568.92626
HSA-MIR-892B98.0067.11821
HSA-MIR-1225-5P96.7666.85417
HSA-MIR-4680-5P96.4367.15893

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 15.1% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 1)

  • MRPL48 is a novel prognostic and predictive biomarker of hepatocellular carcinoma. (PMID:38093387)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriomrpl48ENSDARG00000035167
mus_musculusMrpl48ENSMUSG00000030706
rattus_norvegicusMrpl48ENSRNOG00000018042
drosophila_melanogastermRpL48FBGN0031357
caenorhabditis_elegansWBGENE00016989

Protein

Protein identifiers

Large ribosomal subunit protein mL48Q96GC5 (reviewed: Q96GC5)

Alternative names: 39S ribosomal protein L48, mitochondrial

All UniProt accessions (10): Q96GC5, A0A140TA24, F5GWB4, F5GZH8, F5H1L2, F5H471, F5H4A2, F5H702, F5H717, F5H8D0

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. mL48 is located at the central protuberance. Interacts with OXA1L.

Subcellular location. Mitochondrion.

Similarity. Belongs to the mitochondrion-specific ribosomal protein mL48 family.

Isoforms (2)

UniProt IDNamesCanonical?
Q96GC5-11yes
Q96GC5-32

RefSeq proteins (4): NP_001305427, NP_001305428, NP_001305429, NP_057139* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR027486Ribosomal_uS10_domDomain
IPR027487Ribosomal_mL48Family
IPR036838Ribosomal_uS10_dom_sfHomologous_superfamily

Pfam: PF00338

UniProt features (14 total): strand 5, helix 3, transit peptide 1, chain 1, modified residue 1, splice variant 1, sequence variant 1, turn 1

Structure

Experimental structures (PDB)

83 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-Q96GC5-F176.450.39

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): 199

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: 159 (showing top): HORIUCHI_WTAP_TARGETS_DN, PAL_PRMT5_TARGETS_UP, GRAESSMANN_APOPTOSIS_BY_SERUM_DEPRIVATION_DN, GOBP_MITOCHONDRIAL_TRANSLATION, chr11q13, GOBP_TRANSLATION, JAZAG_TGFB1_SIGNALING_VIA_SMAD4_UP, GOCC_MITOCHONDRIAL_ENVELOPE, GARCIA_TARGETS_OF_FLI1_AND_DAX1_DN, AFP1_Q6, LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_DN, AACTGGA_MIR145, NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_UP, GOCC_LARGE_RIBOSOMAL_SUBUNIT, GOCC_RIBOSOME

GO Biological Process (1): mitochondrial translation (GO:0032543)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (6): mitochondrion (GO:0005739), mitochondrial inner membrane (GO:0005743), mitochondrial ribosome (GO:0005761), 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
binding1
cytoplasm1
intracellular membrane-bounded organelle1
organelle inner membrane1
mitochondrial membrane1
organellar ribosome1
mitochondrial matrix1
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
MRPL48MRPL51Q4U2R6710
MRPL48MRPL45Q9BRJ2646
MRPL48MRPL49Q13405618
MRPL48MRPL20Q9BYC9596
MRPL48MRPL4Q9BYD3585
MRPL48DAP3P51398575
MRPL48MRPS18BQ9Y676558
MRPL48ELOF1P60002547
MRPL48MICOS10Q5TGZ0543
MRPL48MRPL40Q9NQ50540
MRPL48ERAL1O75616536
MRPL48PTCD3Q96EY7519
MRPL48MRPL13Q9BYD1505
MRPL48MRPS22P82650494
MRPL48MPV17L2Q567V2489

IntAct

131 interactions, top by confidence:

ABTypeScore
YBX1HNRNPRpsi-mi:“MI:0914”(association)0.770
MRPS30GTPBP10psi-mi:“MI:0914”(association)0.640
IGF2BP1IGF2BP3psi-mi:“MI:0914”(association)0.640
LIN28AIGF2BP3psi-mi:“MI:0914”(association)0.640
NPKPNA6psi-mi:“MI:0914”(association)0.550
KSR2POLR3Apsi-mi:“MI:0914”(association)0.530
MRPL50GTPBP10psi-mi:“MI:0914”(association)0.530
RPL18NOP56psi-mi:“MI:0914”(association)0.530
MRPL46NDUFAB1psi-mi:“MI:0914”(association)0.530
MRPL10ZZEF1psi-mi:“MI:0914”(association)0.530
MRPL42GATCpsi-mi:“MI:0914”(association)0.530
MRPL41MRPL3psi-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
MRPL48psi-mi:“MI:0915”(physical association)0.370
Papss1TCOF1psi-mi:“MI:0914”(association)0.350
Shoc2GABPB1psi-mi:“MI:0914”(association)0.350
Rpl35RPS6psi-mi:“MI:0914”(association)0.350
Kifc5bKPNA3psi-mi:“MI:0914”(association)0.350
Cbx1psi-mi:“MI:0914”(association)0.350

BioGRID (204): MRPL48 (Affinity Capture-MS), MRPL48 (Affinity Capture-MS), MRPL48 (Affinity Capture-MS), MRPL48 (Affinity Capture-MS), MRPL48 (Affinity Capture-MS), MRPL48 (Affinity Capture-MS), MRPL48 (Affinity Capture-MS), MRPL48 (Affinity Capture-MS), MRPL48 (Affinity Capture-MS), MRPL48 (Affinity Capture-MS), MRPL48 (Co-fractionation), MRPL55 (Co-fractionation), SDHB (Co-fractionation), MRPL48 (Affinity Capture-MS), MRPL48 (Affinity Capture-MS)

ESM2 similar proteins: A6ZPE1, A7TQZ1, B3LJX0, B4JWR9, C4R0B5, C4R8C9, C4XW03, C5DKM2, C5DYE7, C5E3P3, C6Y4D2, C7GNV5, C8ZH56, O13744, O13882, O14006, O60186, O74356, O74464, O94150, P21560, P25642, P36520, P42797, P42847, P53266, Q08774, Q09142, Q09705, Q09759, Q10234, Q10325, Q2YDI5, Q54WP3, Q6BIJ5, Q6BMB3, Q6CJ65, Q6CJB5, Q6FL25, Q6FL71

Diamond homologs: Q2YDI5, Q8JZS9, Q96GC5

SIGNOR signaling

1 interactions.

AEffectBMechanism
MRPL48“form complex”“39S mitochondrial large ribosomal subunit”binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 128 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 control3445.4×5e-47
Mitochondrial translation2943.4×1e-39
Mitochondrial translation initiation3142.8×5e-42
Mitochondrial translation elongation3142.8×5e-42
Mitochondrial translation termination3137.0×7e-40
Translation3322.3×1e-34
Peptide chain elongation1317.9×8e-12
Viral mRNA Translation1317.9×8e-12

GO biological processes:

GO termPartnersFoldFDR
mitochondrial translation3554.3×2e-50
mitochondrial large ribosomal subunit assembly544.2×7e-06
translation3027.5×5e-33
cytoplasmic translation1423.1×2e-13
negative regulation of translation1119.2×1e-09

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance24
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1438 predictions. Top by Δscore:

VariantEffectΔscore
11:73825766:A:Tdonor_gain1.0000
11:73844793:T:TAacceptor_gain1.0000
11:73844802:TTCA:Tacceptor_loss1.0000
11:73844803:TCAGC:Tacceptor_loss1.0000
11:73844804:CAGCC:Cacceptor_loss1.0000
11:73844805:A:AGacceptor_gain1.0000
11:73844806:G:GAacceptor_gain1.0000
11:73844806:GC:Gacceptor_gain1.0000
11:73844806:GCC:Gacceptor_gain1.0000
11:73844806:GCCC:Gacceptor_gain1.0000
11:73844806:GCCCA:Gacceptor_gain1.0000
11:73844929:G:GGdonor_gain1.0000
11:73844973:A:Tdonor_gain1.0000
11:73844976:GGTA:Gdonor_loss1.0000
11:73844977:G:GAdonor_loss1.0000
11:73859905:A:AGacceptor_gain1.0000
11:73859906:G:GGacceptor_gain1.0000
11:73864291:CTTAG:Cacceptor_loss1.0000
11:73864294:A:AGacceptor_gain1.0000
11:73864294:AGCAC:Aacceptor_loss1.0000
11:73864295:G:GAacceptor_gain1.0000
11:73864295:GC:Gacceptor_gain1.0000
11:73864295:GCA:Gacceptor_gain1.0000
11:73864295:GCAC:Gacceptor_gain1.0000
11:73864295:GCACA:Gacceptor_gain1.0000
11:73823347:G:GTdonor_gain0.9900
11:73825702:TTTTA:Tacceptor_loss0.9900
11:73825703:TTTAG:Tacceptor_loss0.9900
11:73825704:TTAG:Tacceptor_loss0.9900
11:73825705:TAGGT:Tacceptor_loss0.9900

AlphaMissense

1376 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
11:73860005:T:AV157D0.984
11:73859999:G:CR155P0.982
11:73844945:T:CC114R0.981
11:73844947:C:GC114W0.968
11:73844943:T:CL113P0.966
11:73844975:A:CS124R0.966
11:73859907:T:AS124R0.966
11:73859907:T:GS124R0.966
11:73844934:T:AV110D0.963
11:73864328:A:CK199N0.963
11:73864328:A:TK199N0.963
11:73844889:T:CL95P0.958
11:73844946:G:AC114Y0.956
11:73863242:T:AV182D0.954
11:73864321:G:CR197P0.954
11:73859912:C:AA126E0.952
11:73844924:G:CA107P0.951
11:73844881:T:AN92K0.947
11:73844881:T:GN92K0.947
11:73844894:G:CA97P0.947
11:73860008:A:CQ158P0.946
11:73863238:G:AG181R0.942
11:73863238:G:CG181R0.942
11:73859984:T:CL150P0.938
11:73844883:T:AI93N0.933
11:73844895:C:AA97E0.932
11:73844967:T:AV121D0.927
11:73863173:T:AI159N0.927
11:73859992:C:GH153D0.926
11:73864320:C:GR197G0.926

dbSNP variants (sampled 300 via entrez): RS1000063933 (11:73837878 C>T), RS1000064498 (11:73827277 G>A,C), RS1000141840 (11:73787124 T>C), RS1000148895 (11:73853157 A>C,G), RS1000180415 (11:73852873 A>C), RS1000210691 (11:73796857 G>A), RS1000220801 (11:73844677 G>A), RS1000233101 (11:73808163 C>G,T), RS1000242111 (11:73794227 TCTAA>T), RS1000242922 (11:73799490 G>A), RS1000259462 (11:73845963 G>A), RS1000289959 (11:73806421 G>A,T), RS1000322032 (11:73824480 G>T), RS1000331239 (11:73851373 T>TA), RS1000341987 (11:73806170 T>C)

Disease associations

OMIM: gene MIM:611853 | 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
GCST001762_405Obesity-related traits4.000000e-06
GCST005231_56Major depressive disorder2.000000e-07
GCST005760_4Dimensional psychopathology (Cognitive)2.000000e-07

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0003939energy intake
EFO:0009098cognitive domain measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

23 total (human), top 23 by PubMed support.

ChemicalActions (top 5)PubMed papers
Air Pollutantsaffects expression, increases abundance, decreases expression2
bisphenol Fincreases expression, affects cotreatment1
dicrotophosdecreases expression1
arseniteaffects binding, increases reaction1
sodium arseniteaffects cotreatment, increases abundance, increases expression1
di-n-butylphosphoric acidaffects expression1
perfluorooctane sulfonic acidincreases expression1
2-palmitoylglycerolincreases expression1
ICG 001decreases expression1
bisphenol Bincreases expression1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic aciddecreases expression1
Acetaminophendecreases expression1
Arsenicaffects cotreatment, increases abundance, increases expression1
Benzo(a)pyreneaffects methylation1
Dexamethasoneaffects cotreatment, increases expression1
Indomethacinaffects cotreatment, increases expression1
Ozoneaffects expression, increases abundance1
Ribonucleotidesaffects binding1
Tretinoindecreases expression1
1-Methyl-3-isobutylxanthineaffects cotreatment, increases expression1
Antirheumatic Agentsincreases expression1
tert-Butylhydroperoxidedecreases expression1
Particulate Matterdecreases expression, increases abundance1

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.