MRPL20

gene
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Also known as FLJ10024bL20m

Summary

MRPL20 (mitochondrial ribosomal protein L20, HGNC:14478) is a protein-coding gene on chromosome 1p36.33, encoding Large ribosomal subunit protein bL20m (Q9BYC9). It is a selective cancer dependency (DepMap: 37.6% 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 39S subunit protein. A pseudogene corresponding to this gene is found on chromosome 21q. Alternative splicing results in multiple transcript variants encoding different isoforms.

Source: NCBI Gene 55052 — RefSeq curated summary.

At a glance

  • GWAS associations: 3
  • Clinical variants (ClinVar): 46 total
  • Cancer dependency (DepMap): dependent in 37.6% of screened cell lines
  • MANE Select transcript: NM_017971

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:14478
Approved symbolMRPL20
Namemitochondrial ribosomal protein L20
Location1p36.33
Locus typegene with protein product
StatusApproved
AliasesFLJ10024, bL20m
Ensembl geneENSG00000242485
Ensembl biotypeprotein_coding
OMIM611833
Entrez55052

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 10 protein_coding, 2 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000344843, ENST00000477686, ENST00000482352, ENST00000487659, ENST00000492508, ENST00000493287, ENST00000872275, ENST00000872276, ENST00000872277, ENST00000914256, ENST00000914257, ENST00000914258, ENST00000914259

RefSeq mRNA: 2 — MANE Select: NM_017971 NM_001318485, NM_017971

CCDS: CCDS26

Canonical transcript exons

ENST00000344843 — 4 exons

ExonStartEnd
ENSE0000173503414071311407293
ENSE0000194054514019091402256
ENSE0000347895514058091405886
ENSE0000348046814069091407019

Expression profiles

Bgee: expression breadth ubiquitous, 288 present calls, max score 99.61.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 110.6662 / max 489.9961, expressed in 1828 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
9781110.66621828

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
palpebral conjunctivaUBERON:000181299.61gold quality
epithelium of nasopharynxUBERON:000195199.30gold quality
germinal epithelium of ovaryUBERON:000130499.28gold quality
esophagus squamous epitheliumUBERON:000692099.15gold quality
cervix squamous epitheliumUBERON:000692298.98gold quality
squamous epitheliumUBERON:000691498.96gold quality
gingival epitheliumUBERON:000194998.95gold quality
epithelium of esophagusUBERON:000197698.77gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451198.76gold quality
gingivaUBERON:000182898.57gold quality
hindlimb stylopod muscleUBERON:000425298.55gold quality
amniotic fluidUBERON:000017398.54gold quality
corpus epididymisUBERON:000435998.53gold quality
mucosa of paranasal sinusUBERON:000503098.51gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450298.46gold quality
Brodmann (1909) area 23UBERON:001355498.45gold quality
parietal pleuraUBERON:000240098.43gold quality
endothelial cellCL:000011598.41gold quality
biceps brachiiUBERON:000150798.38gold quality
heart right ventricleUBERON:000208098.38gold quality
adult organismUBERON:000702398.38gold quality
oral cavityUBERON:000016798.32gold quality
gastrocnemiusUBERON:000138898.31gold quality
pigmented layer of retinaUBERON:000178298.29gold quality
muscle of legUBERON:000138398.28gold quality
vastus lateralisUBERON:000137998.27gold quality
adenohypophysisUBERON:000219698.26gold quality
caput epididymisUBERON:000435898.26gold quality
cardiac ventricleUBERON:000208298.23gold quality
heart left ventricleUBERON:000208498.23gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3no0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

24 targeting MRPL20, 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-548AJ-3P99.9673.385345
HSA-MIR-548X-3P99.9673.385345
HSA-MIR-551B-5P99.9671.283493
HSA-MIR-548J-3P99.9472.614881
HSA-MIR-548AE-3P99.9372.664867
HSA-MIR-548AH-3P99.9372.544872
HSA-MIR-548AM-3P99.9372.544872
HSA-MIR-548AQ-3P99.9372.664867
HSA-MIR-548AR-3P99.8571.263889
HSA-MIR-548AZ-3P99.8270.563549
HSA-MIR-548BC99.8270.613524
HSA-MIR-548E-3P99.8270.593514
HSA-MIR-548F-3P99.8270.593540
HSA-MIR-57799.7869.132479
HSA-MIR-548A-3P99.7670.583524
HSA-MIR-1213099.7565.47452
HSA-MIR-4802-3P99.7270.131273
HSA-MIR-377-3P99.3770.181905
HSA-MIR-431699.3765.751360
HSA-MIR-520F-5P99.3470.401632
HSA-MIR-3940-5P99.1465.26493
HSA-MIR-450799.1465.27515
HSA-MIR-548L99.0670.902560
HSA-MIR-393596.3366.79797

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 37.6% of screened cell lines.

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriomrpl20ENSDARG00000090462
mus_musculusMrpl20ENSMUSG00000029066
rattus_norvegicusMrpl20ENSRNOG00000018647
drosophila_melanogastermRpL20FBGN0036335
caenorhabditis_elegansWBGENE00012992

Protein

Protein identifiers

Large ribosomal subunit protein bL20mQ9BYC9 (reviewed: Q9BYC9)

Alternative names: 39S ribosomal protein L20, mitochondrial

All UniProt accessions (2): I3L2X1, Q9BYC9

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. Interacts with OXA1L.

Subcellular location. Mitochondrion.

Similarity. Belongs to the bacterial ribosomal protein bL20 family.

Isoforms (2)

UniProt IDNamesCanonical?
Q9BYC9-11yes
Q9BYC9-22

RefSeq proteins (2): NP_001305414, NP_060441* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR005813Ribosomal_bL20Family
IPR035566Ribosomal_protein_bL20_CHomologous_superfamily

Pfam: PF00453

UniProt features (12 total): helix 6, turn 2, transit peptide 1, chain 1, strand 1, splice variant 1

Structure

Experimental structures (PDB)

86 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
8QU1ELECTRON MICROSCOPY2.74
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

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9BYC9-F190.900.80

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: 149 (showing top): PAL_PRMT5_TARGETS_UP, GOBP_MITOCHONDRIAL_TRANSLATION, GOBP_TRANSLATION, GOMF_STRUCTURAL_CONSTITUENT_OF_RIBOSOME, GOCC_MITOCHONDRIAL_ENVELOPE, GARY_CD5_TARGETS_DN, TIEN_INTESTINE_PROBIOTICS_24HR_UP, BURTON_ADIPOGENESIS_5, GRYDER_PAX3FOXO1_ENHANCERS_IN_TADS, MULLIGAN_NTF3_SIGNALING_VIA_INSR_AND_IGF1R_UP, GOCC_LARGE_RIBOSOMAL_SUBUNIT, GOCC_RIBOSOME, GRYDER_PAX3FOXO1_TOP_ENHANCERS, GOCC_ORGANELLAR_RIBOSOME, GOCC_MITOCHONDRIAL_MATRIX

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

GO Molecular Function (4): RNA binding (GO:0003723), structural constituent of ribosome (GO:0003735), rRNA binding (GO:0019843), 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
peptidyltransferase activity1
translational initiation1
translational elongation1
translational termination1
macromolecule biosynthetic process1
protein metabolic process1
protein biosynthetic process1
nucleic acid binding1
structural molecule activity1
ribosome1
RNA binding1
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

2897 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
MRPL20MRPL51Q4U2R6689
MRPL20MRPL33O75394645
MRPL20MTERF3Q96E29626
MRPL20MRPL24Q96A35626
MRPL20MRPL47Q9HD33619
MRPL20MRPL48Q96GC5596
MRPL20MRPL23Q16540587
MRPL20MRPL13Q9BYD1574
MRPL20MRPL12P52815573
MRPL20NDUFB9Q9Y6M9567
MRPL20MRPL49Q13405559
MRPL20MRPL34Q9BQ48557
MRPL20MRPS7Q9Y2R9548
MRPL20MRPL41Q8IXM3548
MRPL20MRPS9P82933544

IntAct

164 interactions, top by confidence:

ABTypeScore
MIS12ZWINTpsi-mi:“MI:0914”(association)0.900
YBX1HNRNPRpsi-mi:“MI:0914”(association)0.770
MRPS30GTPBP10psi-mi:“MI:0914”(association)0.640
MRPL50GTPBP10psi-mi:“MI:0914”(association)0.530
RPL18NOP56psi-mi:“MI:0914”(association)0.530
MRPL10ZZEF1psi-mi:“MI:0914”(association)0.530
MRPL42GATCpsi-mi:“MI:0914”(association)0.530
PEX19FAM20Bpsi-mi:“MI:0914”(association)0.530
MRPL41MRPL3psi-mi:“MI:0914”(association)0.530
YBX1IGF2BP3psi-mi:“MI:0914”(association)0.530
MRPL2GTPBP10psi-mi:“MI:0914”(association)0.530
CASQ2PES1psi-mi:“MI:0914”(association)0.530
RHOT2UBCpsi-mi:“MI:0914”(association)0.530
MRPL13GTPBP10psi-mi:“MI:0914”(association)0.530
MRPL18GTPBP10psi-mi:“MI:0914”(association)0.530
IPO5SLC27A2psi-mi:“MI:0914”(association)0.530
PEX19MYO1Dpsi-mi:“MI:0914”(association)0.530
RPL19ZBTB24psi-mi:“MI:0914”(association)0.530
RPL27AMRPS9psi-mi:“MI:0914”(association)0.530
RPL13ANVLpsi-mi:“MI:0914”(association)0.530
PRR3MRPS14psi-mi:“MI:0914”(association)0.530
MRPL27MRPL33psi-mi:“MI:0914”(association)0.530

BioGRID (215): MRPL20 (Affinity Capture-MS), MRPL20 (Affinity Capture-MS), MRPL20 (Affinity Capture-MS), MRPL20 (Affinity Capture-MS), MRPL20 (Affinity Capture-MS), MRPL20 (Affinity Capture-MS), MRPL20 (Affinity Capture-MS), MRPL20 (Affinity Capture-MS), MRPL20 (Affinity Capture-MS), MRPL20 (Affinity Capture-MS), MRPL20 (Affinity Capture-MS), MRPL20 (Affinity Capture-MS), MRPL20 (Co-fractionation), MRPL20 (Co-fractionation), MRPL20 (Co-fractionation)

ESM2 similar proteins: A0AJY7, B1VKG7, O60783, P56556, P82915, P82920, P82933, Q02366, Q0MQA3, Q0MQA4, Q0MQA5, Q0VFH6, Q13084, Q19V89, Q1JQ99, Q29IK4, Q2HJJ1, Q2TA12, Q2TBR2, Q3T040, Q3T0J3, Q498T4, Q58DQ5, Q58DV5, Q5I0K8, Q5T653, Q5U4Z8, Q5ZMU0, Q6B860, Q6DDY9, Q6P1L8, Q71YD4, Q7M0E7, Q7SF85, Q7ZUH5, Q80X85, Q8MFA1, Q8Y620, Q92AC7, Q9BYC9

Diamond homologs: A0KWV7, A0L4J9, A1ARE2, A1K4E4, A1RJI6, A1S6G7, A1SWU2, A3D4I5, A3QEJ7, A4G616, A4Y703, A5EZ15, A5VT72, A6SY33, A6WNG9, A7HPK9, A7N012, A8FV59, A8H4U3, A9L2Q6, A9M9V2, B0CJL8, B0TT23, B1KG58, B1XYZ6, B1YP16, B2A5N9, B2J0D0, B2S9B6, B2SZF9, B2UGJ5, B3E1T8, B3PYE1, B3R4J4, B4RSL5, B4UAN7, B5EBY2, B5ZXR9, B6EN31, B6IPJ8

SIGNOR signaling

1 interactions.

AEffectBMechanism
MRPL20“form complex”“39S mitochondrial large ribosomal subunit”binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 142 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 control3844.0×3e-52
Mitochondrial translation3241.5×5e-43
Mitochondrial translation initiation3440.7×2e-45
Mitochondrial translation elongation3440.7×2e-45
Mitochondrial translation termination3435.2×5e-43
Translation3319.3×4e-32
ZNF598 and the Ribosome-associated Quality Trigger (RQT) complex dissociate a ribosome stalled on a no-go mRNA1011.1×2e-06
Peptide chain elongation910.8×8e-06

GO biological processes:

GO termPartnersFoldFDR
mitochondrial translation3648.1×1e-49
mitochondrial large ribosomal subunit assembly645.8×5e-07
translation2822.1×1e-27
cytoplasmic translation912.8×5e-06
negative regulation of translation710.6×6e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance37
Likely benign2
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

446 predictions. Top by Δscore:

VariantEffectΔscore
1:1402252:TGGCA:Tacceptor_gain1.0000
1:1402253:GGCA:Gacceptor_gain1.0000
1:1402254:GCA:Gacceptor_gain1.0000
1:1402255:CAC:Cacceptor_gain1.0000
1:1402257:C:CCacceptor_gain1.0000
1:1405813:A:Cdonor_gain1.0000
1:1406907:ACGGT:Adonor_gain1.0000
1:1406908:CGGTC:Cdonor_gain1.0000
1:1407127:TCACC:Tdonor_loss1.0000
1:1407128:CA:Cdonor_loss1.0000
1:1407129:A:ACdonor_gain1.0000
1:1407129:AC:Adonor_gain1.0000
1:1407129:ACC:Adonor_gain1.0000
1:1407130:C:CTdonor_gain1.0000
1:1407130:CC:Cdonor_gain1.0000
1:1407130:CCC:Cdonor_gain1.0000
1:1407130:CCCT:Cdonor_gain1.0000
1:1407130:CCCTG:Cdonor_gain1.0000
1:1407150:T:TAdonor_gain1.0000
1:1402255:CA:Cacceptor_gain0.9900
1:1405841:T:TAdonor_gain0.9900
1:1405882:CAGAG:Cacceptor_gain0.9900
1:1405883:AGAGC:Aacceptor_loss0.9900
1:1405886:GC:Gacceptor_loss0.9900
1:1405887:C:CAacceptor_loss0.9900
1:1405887:C:CCacceptor_gain0.9900
1:1406908:CGGT:Cdonor_gain0.9900
1:1407016:AGTG:Aacceptor_gain0.9900
1:1407018:TG:Tacceptor_gain0.9900
1:1407020:C:CCacceptor_gain0.9900

AlphaMissense

960 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
1:1402194:G:CF113L0.985
1:1402194:G:TF113L0.985
1:1402196:A:GF113L0.985
1:1407014:G:CF31L0.984
1:1407014:G:TF31L0.984
1:1407016:A:GF31L0.984
1:1405857:G:CS76R0.981
1:1405857:G:TS76R0.981
1:1405859:T:GS76R0.981
1:1402216:G:TA106D0.980
1:1407135:G:TA28D0.972
1:1402219:A:GL105P0.971
1:1405861:G:TA75D0.971
1:1402243:A:TL97H0.970
1:1405873:C:GR71P0.969
1:1402186:A:GL116S0.968
1:1402207:T:AE109V0.968
1:1402195:A:GF113S0.967
1:1402217:C:GA106P0.965
1:1406982:G:TA42E0.965
1:1402226:C:GA103P0.962
1:1405816:A:GL90S0.959
1:1406937:C:GR57P0.958
1:1405828:A:GL86P0.955
1:1406993:G:CC38W0.955
1:1402174:G:TA120D0.948
1:1406962:C:GA49P0.948
1:1402184:C:GA117P0.947
1:1402240:T:AN98I0.947
1:1402183:G:TA117D0.946

dbSNP variants (sampled 300 via entrez): RS1000250273 (1:1407270 T>C), RS1000429563 (1:1403650 A>G), RS1000584590 (1:1406503 C>T), RS1000635236 (1:1406314 C>A,G), RS1000693960 (1:1402447 G>A,C), RS1000759461 (1:1403440 C>T), RS1001086226 (1:1409003 G>A,C), RS1001121972 (1:1409162 G>A), RS1001424518 (1:1408091 G>C), RS1001900382 (1:1407312 C>G), RS1002255236 (1:1405553 C>A,T), RS1002437457 (1:1401741 A>G), RS1002585731 (1:1404683 G>A,C), RS1002944964 (1:1403064 G>A), RS1003145746 (1:1407442 A>C)

Disease associations

OMIM: gene MIM:611833 | 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
GCST004131_103Inflammatory bowel disease2.000000e-07
GCST004133_40Ulcerative colitis3.000000e-06
GCST007268_75Diastolic blood pressure2.000000e-08

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0006336diastolic blood pressure

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
sodium arsenitedecreases expression, increases expression2
alpha phellandrenedecreases expression1
bisphenol Adecreases expression1
arseniteaffects binding, increases reaction1
tris(1,3-dichloro-2-propyl)phosphatedecreases expression1
cobaltous chloridedecreases expression1
di-n-butylphosphoric acidaffects expression1
corosolic aciddecreases expression1
K 7174decreases expression1
erucylphospho-N,N,N-trimethylpropylammoniumdecreases expression1
Grape Seed Proanthocyanidinsaffects cotreatment, decreases expression1
Resveratrolincreases expression, affects cotreatment1
Acetaminophendecreases expression, affects cotreatment1
Atrazinedecreases expression1
Benzo(a)pyrenedecreases methylation1
Cadmiumincreases abundance, increases expression1
Catechinaffects cotreatment, decreases expression1
Diazinonincreases methylation1
Hydrogen Peroxideaffects expression1
Lipopolysaccharidesaffects cotreatment, decreases expression1
Nickelincreases expression1
Plant Extractsaffects cotreatment, increases expression1
Quercetindecreases expression1
Ribonucleotidesaffects binding1
Silicon Dioxidedecreases expression1
Smokedecreases expression1
Thiramdecreases expression1
Tunicamycindecreases expression1
Urethanedecreases expression1
Valproic Acidincreases methylation1

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.