MRPL42

gene
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Also known as MRPS32MRP-L31RPML31PTD007HSPC204MRPL31mL42

Summary

MRPL42 (mitochondrial ribosomal protein L42, HGNC:14493) is a protein-coding gene on chromosome 12q22, encoding Large ribosomal subunit protein mL42 (Q9Y6G3).

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 protein identified as belonging to both the 28S and the 39S subunits. Alternative splicing results in multiple transcript variants. Pseudogenes corresponding to this gene are found on chromosomes 4q, 6p, 6q, 7p, and 15q.

Source: NCBI Gene 28977 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): complex neurodevelopmental disorder (Limited, GenCC)
  • GWAS associations: 3
  • Clinical variants (ClinVar): 32 total — 1 pathogenic
  • MANE Select transcript: NM_014050

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:14493
Approved symbolMRPL42
Namemitochondrial ribosomal protein L42
Location12q22
Locus typegene with protein product
StatusApproved
AliasesMRPS32, MRP-L31, RPML31, PTD007, HSPC204, MRPL31, mL42
Ensembl geneENSG00000198015
Ensembl biotypeprotein_coding
OMIM611847
Entrez28977

Gene structure

Transcript identifiers

Ensembl transcripts: 26 — 21 protein_coding, 3 nonsense_mediated_decay, 2 protein_coding_CDS_not_defined

ENST00000358678, ENST00000393128, ENST00000547098, ENST00000548545, ENST00000549561, ENST00000549982, ENST00000551396, ENST00000552217, ENST00000552326, ENST00000552938, ENST00000873991, ENST00000873992, ENST00000873993, ENST00000873994, ENST00000873995, ENST00000873996, ENST00000873997, ENST00000873998, ENST00000919736, ENST00000919737, ENST00000919738, ENST00000919739, ENST00000919740, ENST00000919741, ENST00000919742, ENST00000919743

RefSeq mRNA: 2 — MANE Select: NM_014050 NM_014050, NM_172177

CCDS: CCDS9045

Canonical transcript exons

ENST00000549982 — 6 exons

ExonStartEnd
ENSE000023673959346751493467554
ENSE000023897949350117693516214
ENSE000035037589347695493477017
ENSE000035206969348749793487660
ENSE000035524769346919293469355
ENSE000036095499347938893479472

Expression profiles

Bgee: expression breadth ubiquitous, 284 present calls, max score 97.87.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 39.7601 / max 1099.5960, expressed in 1802 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
12735136.44751801
1273503.31261408

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
adrenal tissueUBERON:001830397.87gold quality
islet of LangerhansUBERON:000000697.44gold quality
ganglionic eminenceUBERON:000402396.27gold quality
rectumUBERON:000105295.51gold quality
embryoUBERON:000092294.86gold quality
spermCL:000001994.55gold quality
endothelial cellCL:000011594.44gold quality
ventricular zoneUBERON:000305394.02gold quality
right testisUBERON:000453493.77gold quality
left testisUBERON:000453393.75gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099193.70gold quality
right adrenal gland cortexUBERON:003582793.37gold quality
heart right ventricleUBERON:000208093.25gold quality
left ventricle myocardiumUBERON:000656693.21gold quality
testisUBERON:000047393.14gold quality
male germ cellCL:000001593.10gold quality
calcaneal tendonUBERON:000370193.06gold quality
right adrenal glandUBERON:000123392.96gold quality
myocardiumUBERON:000234992.80gold quality
left adrenal glandUBERON:000123492.77gold quality
adrenal glandUBERON:000236992.47gold quality
mucosa of sigmoid colonUBERON:000499392.46gold quality
gall bladderUBERON:000211092.32gold quality
stromal cell of endometriumCL:000225592.29gold quality
left adrenal gland cortexUBERON:003582592.28gold quality
smooth muscle tissueUBERON:000113592.19gold quality
cardiac muscle of right atriumUBERON:000337992.07gold quality
colonic mucosaUBERON:000031792.04gold quality
olfactory segment of nasal mucosaUBERON:000538691.95gold quality
endometriumUBERON:000129591.91gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes14.44
E-MTAB-6819no1217.60
E-MTAB-9388no13.82

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): TP63

miRNA regulators (miRDB)

98 targeting MRPL42, 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-6740-5P100.0065.64932
HSA-MIR-3646100.0073.565283
HSA-MIR-1277-5P100.0073.955056
HSA-MIR-6833-3P100.0070.633197
HSA-MIR-8485100.0077.574731
HSA-MIR-4768-5P100.0069.492861
HSA-MIR-548P99.9872.253784
HSA-MIR-3688-3P99.9772.022834
HSA-MIR-314899.9775.066478
HSA-MIR-302E99.9670.742669
HSA-MIR-1468-3P99.9672.743797
HSA-MIR-590-3P99.9674.346478
HSA-MIR-96-5P99.9572.802140
HSA-MIR-101-3P99.9475.032230
HSA-MIR-335-3P99.9373.364958
HSA-MIR-539-5P99.9370.302855
HSA-MIR-314399.9371.963104
HSA-MIR-6835-3P99.9370.492904
HSA-MIR-1213399.9271.822006
HSA-MIR-6508-5P99.9270.672465
HSA-MIR-1271-5P99.9171.991972
HSA-MIR-6809-3P99.9171.453814
HSA-MIR-374A-5P99.9071.342923
HSA-MIR-374B-5P99.9069.982734
HSA-MIR-302A-3P99.8971.231777
HSA-MIR-302B-3P99.8971.231777
HSA-MIR-302C-3P99.8971.201778
HSA-MIR-302D-3P99.8971.251777
HSA-MIR-153-5P99.8973.866317
HSA-MIR-806799.8669.592260

Literature-anchored findings (GeneRIF, showing 2)

  • MPO and BPI in CD4(+)T-lymphocytes, and PDHA1 and MRPL42 in CD8(+) T-lymphocytes might be used as specific biomarkers of severe asthma progression. (PMID:26107902)
  • MRPL42 is a novel oncogene in glioma and might help us develop promising targetted therapies for glioma patients. (PMID:29531015)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
mus_musculusMrpl42ENSMUSG00000062981
rattus_norvegicusMrpl42l1ENSRNOG00000025964
rattus_norvegicusENSRNOG00000031132
rattus_norvegicusMrpl42ENSRNOG00000042740

Protein

Protein identifiers

Large ribosomal subunit protein mL42Q9Y6G3 (reviewed: Q9Y6G3)

Alternative names: 39S ribosomal protein L31, mitochondrial, 39S ribosomal protein L42, mitochondrial

All UniProt accessions (6): Q9Y6G3, F8VVR0, J3KP21, J3KPP0, S4R2Z7, S4R360

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 mL42 family.

RefSeq proteins (2): NP_054769, NP_751917 (=MANE)

Domains & families (InterPro)

IDNameType
IPR019346Ribosomal_mL42Family

Pfam: PF10210

UniProt features (9 total): helix 4, strand 3, transit peptide 1, chain 1

Structure

Experimental structures (PDB)

85 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-Q9Y6G3-F175.260.41

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: 182 (showing top): RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP, STARK_PREFRONTAL_CORTEX_22Q11_DELETION_DN, CHIANG_LIVER_CANCER_SUBCLASS_UNANNOTATED_DN, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GOBP_MITOCHONDRIAL_TRANSLATION, PATIL_LIVER_CANCER, GOBP_TRANSLATION, WEI_MYCN_TARGETS_WITH_E_BOX, ROZANOV_MMP14_TARGETS_UP, GOMF_STRUCTURAL_CONSTITUENT_OF_RIBOSOME, MODULE_206, GOCC_MITOCHONDRIAL_ENVELOPE, DODD_NASOPHARYNGEAL_CARCINOMA_UP, MAYBURD_RESPONSE_TO_L663536_DN

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

GO Molecular Function (2): RNA binding (GO:0003723), structural constituent of ribosome (GO:0003735)

GO Cellular Component (8): mitochondrion (GO:0005739), mitochondrial inner membrane (GO:0005743), mitochondrial large ribosomal subunit (GO:0005762), mitochondrial small ribosomal subunit (GO:0005763), plasma membrane (GO:0005886), ribosome (GO:0005840), membrane (GO:0016020), 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
mitochondrial ribosome2
mitochondrial protein-containing complex2
peptidyltransferase activity1
translational initiation1
translational elongation1
translational termination1
macromolecule biosynthetic process1
protein metabolic process1
protein biosynthetic process1
mitochondrion1
translation1
mitochondrial gene expression1
nucleic acid binding1
structural molecule activity1
ribosome1
cytoplasm1
intracellular membrane-bounded organelle1
organelle inner membrane1
mitochondrial membrane1
organellar large ribosomal subunit1
organellar small ribosomal subunit1
membrane1
cell periphery1
intracellular membraneless organelle1
cellular anatomical structure1
protein-containing complex1

Protein interactions and networks

STRING

1484 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
MRPL42KGD4P82909630
MRPL42MRPL37Q9BZE1615
MRPL42DAP3P51398589
MRPL42MRPS18CQ9Y3D5587
MRPL42MRPL41Q8IXM3585
MRPL42MRPL32Q9BYC8574
MRPL42PTCD3Q96EY7543
MRPL42CHCHD1Q96BP2525
MRPL42MRPL47Q9HD33494
MRPL42QRICH2Q9H0J4491
MRPL42MRPS18BQ9Y676488
MRPL42MRPS18AQ9NVS2488
MRPL42EMC4Q5J8M3486
MRPL42MRPL16Q9NX20484
MRPL42MRPL1Q9BYD6478

IntAct

65 interactions, top by confidence:

ABTypeScore
TEPSINAP4M1psi-mi:“MI:0914”(association)0.700
LIN28AIGF2BP3psi-mi:“MI:0914”(association)0.640
MRPL42GATCpsi-mi:“MI:0914”(association)0.530
YBX1IGF2BP3psi-mi:“MI:0914”(association)0.530
MRPL13GTPBP10psi-mi:“MI:0914”(association)0.530
MRPL18GTPBP10psi-mi:“MI:0914”(association)0.530
ABT1ZNF316psi-mi:“MI:0914”(association)0.530
NDUFAB1MIEF1psi-mi:“MI:0915”(physical association)0.490
revTMED10psi-mi:“MI:0914”(association)0.460
psi-mi:“MI:0914”(association)0.350
ATAD3ATMEM223psi-mi:“MI:0914”(association)0.350
RASA1MYO1Cpsi-mi:“MI:0914”(association)0.350
ARPC2psi-mi:“MI:0914”(association)0.350
H1-7psi-mi:“MI:0914”(association)0.350
S100A2PLEKHG3psi-mi:“MI:0914”(association)0.350
FAM120AGTPBP10psi-mi:“MI:0914”(association)0.350
MRPL33psi-mi:“MI:0914”(association)0.350
MRPL53psi-mi:“MI:0914”(association)0.350
MRPL51psi-mi:“MI:0914”(association)0.350
MRPL42psi-mi:“MI:0914”(association)0.350
MRPL52psi-mi:“MI:0914”(association)0.350
RPL37psi-mi:“MI:0914”(association)0.350
YBX2psi-mi:“MI:0914”(association)0.350
RBMS2ZNF275psi-mi:“MI:0914”(association)0.350
PRR3RBM47psi-mi:“MI:0914”(association)0.350
MRPL42UBA6psi-mi:“MI:0914”(association)0.350
FAHD1VWA8psi-mi:“MI:0914”(association)0.350
NEIL1GTPBP10psi-mi:“MI:0914”(association)0.350

BioGRID (344): MRPL42 (Affinity Capture-MS), MRPL42 (Affinity Capture-MS), MRPL42 (Affinity Capture-MS), MRPL42 (Affinity Capture-MS), MRPL42 (Affinity Capture-MS), MRPL42 (Affinity Capture-MS), MRPL42 (Affinity Capture-MS), MRPL42 (Affinity Capture-MS), MRPL42 (Affinity Capture-MS), MRPL42 (Affinity Capture-MS), MRPL42 (Affinity Capture-MS), MRPL42 (Affinity Capture-MS), MRPL42 (Affinity Capture-MS), MRPS30 (Affinity Capture-MS), MRPL50 (Affinity Capture-MS)

ESM2 similar proteins: A3KP48, A8WGU8, O09111, O43674, O95169, O95178, P0C2B7, P0C2B9, P0CB69, P0CB70, P0CB85, P0CB86, P82649, P82927, P83565, Q02372, Q02380, Q0MQC7, Q0MQC9, Q0MQD6, Q0MQD7, Q0MQD8, Q0MQE6, Q0MQE7, Q0MQF5, Q0MQJ3, Q0MQJ4, Q0MQJ5, Q29259, Q2NKR7, Q4G0I0, Q4QQV3, Q4R4E0, Q5R4S3, Q5R504, Q5RFR4, Q6DQX6, Q6RUT7, Q8HXG5, Q96A26

Diamond homologs: P0C2B9, P82927, Q5R4S3, Q9CPV3, Q9Y6G3

SIGNOR signaling

1 interactions.

AEffectBMechanism
MRPL42“form complex”“39S mitochondrial large ribosomal subunit”binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 66 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 control1850.2×6e-25
Mitochondrial translation1546.9×1e-20
Mitochondrial translation initiation1646.1×1e-21
Mitochondrial translation elongation1646.1×1e-21
Mitochondrial translation termination1639.9×9e-21
Translation1521.2×3e-15

GO biological processes:

GO termPartnersFoldFDR
mitochondrial translation1750.1×1e-22
translation1119.2×1e-09
negative regulation of translation516.6×1e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic1
Likely pathogenic0
Uncertain significance21
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (1)

Variant IDHGVSClassification
4071942NM_014050.4(MRPL42):c.219+6T>APathogenic

SpliceAI

1416 predictions. Top by Δscore:

VariantEffectΔscore
12:93467551:CAAG:Cdonor_loss1.0000
12:93467552:AAGGT:Adonor_loss1.0000
12:93467553:AG:Adonor_loss1.0000
12:93467555:GT:Gdonor_loss1.0000
12:93469356:G:GGdonor_gain1.0000
12:93476940:T:TAacceptor_gain1.0000
12:93476941:G:Aacceptor_gain1.0000
12:93479469:AAAAG:Adonor_loss1.0000
12:93479470:AAA:Adonor_gain1.0000
12:93479471:AAG:Adonor_loss1.0000
12:93479472:AGTA:Adonor_loss1.0000
12:93479473:G:Adonor_loss1.0000
12:93479473:G:GGdonor_gain1.0000
12:93479474:T:Adonor_loss1.0000
12:93487483:T:Aacceptor_gain1.0000
12:93487495:A:AGacceptor_gain1.0000
12:93487496:G:GTacceptor_gain1.0000
12:93487496:GC:Gacceptor_gain1.0000
12:93487496:GCC:Gacceptor_gain1.0000
12:93487496:GCCT:Gacceptor_gain1.0000
12:93487496:GCCTA:Gacceptor_gain1.0000
12:93487656:GGACG:Gdonor_gain1.0000
12:93487657:GACG:Gdonor_gain1.0000
12:93487657:GACGG:Gdonor_gain1.0000
12:93487658:ACG:Adonor_gain1.0000
12:93487659:CG:Cdonor_gain1.0000
12:93487660:GG:Gdonor_gain1.0000
12:93487661:G:GAdonor_loss1.0000
12:93487661:G:GGdonor_gain1.0000
12:93501297:G:GGdonor_gain1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000150608 (12:93497163 T>C), RS1000161991 (12:93497363 A>T), RS1000194108 (12:93489076 TAATG>T), RS1000308793 (12:93513905 C>G), RS1000322548 (12:93495931 TAAA>T), RS1000428127 (12:93489473 A>C,G), RS1000438770 (12:93495742 G>A,C), RS1000458052 (12:93505047 C>T), RS1000508935 (12:93467513 G>A), RS1000515893 (12:93483523 T>G), RS1000683140 (12:93471782 G>A), RS1000731298 (12:93509149 C>T), RS1000764409 (12:93489695 T>C), RS1000902483 (12:93472094 G>A), RS1000914406 (12:93515429 G>A,T)

Disease associations

OMIM: gene MIM:611847 | disease phenotypes:

GenCC curated gene-disease

DiseaseClassificationInheritance
complex neurodevelopmental disorderLimitedAutosomal recessive

Mondo (1): complex neurodevelopmental disorder (MONDO:0100038)

Orphanet (0):

HPO phenotypes

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

GWAS associations

3 associations (top):

StudyTraitp-value
GCST000175_22Height2.000000e-07
GCST005723_3Peanut allergy (maternal genetic effects)9.000000e-06
GCST005991_19Platelet count2.000000e-08

EFO canonical traits (3, from GWAS)

EFO IDTrait name
EFO:0005939parental genotype effect measurement
EFO:0007017peanut allergy measurement
EFO:0004309platelet count

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Air Pollutantsaffects cotreatment, decreases expression, increases abundance, affects expression3
Valproic Acidaffects expression, decreases expression3
sodium arsenitedecreases expression2
Ozoneaffects cotreatment, decreases expression, increases abundance, affects expression2
Tretinoindecreases expression2
dicrotophosdecreases expression1
alpha-pineneaffects cotreatment, decreases expression, increases abundance1
bisphenol Adecreases expression1
beta-lapachoneincreases expression1
arseniteincreases reaction, affects binding1
cobaltous chloridedecreases expression1
perfluorooctanoic aciddecreases expression1
methacrylaldehydeaffects cotreatment, decreases expression, increases abundance1
beta-methylcholineaffects expression1
di-n-butylphosphoric acidaffects expression1
cylindrospermopsinincreases expression1
CGP 52608affects binding, increases reaction1
K 7174decreases expression1
jinfukangdecreases expression1
Temozolomideincreases expression1
Arsenic Trioxidedecreases expression1
Acetaminophendecreases expression1
Acroleinaffects cotreatment, decreases expression, increases abundance1
Atrazinedecreases expression1
Dimethyl Sulfoxidedecreases expression1
Hydrogen Peroxideaffects expression1
Methyl Methanesulfonatedecreases expression1
Ribonucleotidesaffects binding1
Tunicamycindecreases expression1
Aflatoxin B1increases expression1

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT06310681Not specifiedCOMPLETEDPilot Testing of a Co-adapted Group Programme for Parents/Carers of Children With Complex Neurodisability
NCT07303049Not specifiedNOT_YET_RECRUITINGCognitive Benefit of Intensive Rehabilitation Using Rhythmic Music Training in Children With Complex Neurodevelopmental Disorder