MRPL16

gene
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Also known as FLJ20484PNAS-111uL16m

Summary

MRPL16 (mitochondrial ribosomal protein L16, HGNC:14476) is a protein-coding gene on chromosome 11q12.1, encoding Large ribosomal subunit protein uL16m (Q9NX20). It is a selective cancer dependency (DepMap: 56.7% 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.

Source: NCBI Gene 54948 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 47 total
  • Cancer dependency (DepMap): dependent in 56.7% of screened cell lines
  • MANE Select transcript: NM_017840

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:14476
Approved symbolMRPL16
Namemitochondrial ribosomal protein L16
Location11q12.1
Locus typegene with protein product
StatusApproved
AliasesFLJ20484, PNAS-111, uL16m
Ensembl geneENSG00000166902
Ensembl biotypeprotein_coding
OMIM611829
Entrez54948

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 5 protein_coding, 2 retained_intron

ENST00000300151, ENST00000525470, ENST00000531802, ENST00000534340, ENST00000884381, ENST00000923616, ENST00000923617

RefSeq mRNA: 1 — MANE Select: NM_017840 NM_017840

CCDS: CCDS7976

Canonical transcript exons

ENST00000300151 — 4 exons

ExonStartEnd
ENSE000011076155980614059806832
ENSE000011076205981060459810778
ENSE000035837645980770159807849
ENSE000036691195980985559809920

Expression profiles

Bgee: expression breadth ubiquitous, 278 present calls, max score 96.99.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 65.9732 / max 350.5138, expressed in 1822 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
11988165.97321822

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
apex of heartUBERON:000209896.99gold quality
right adrenal glandUBERON:000123396.42gold quality
heart left ventricleUBERON:000208496.26gold quality
cardiac ventricleUBERON:000208296.23gold quality
mucosa of transverse colonUBERON:000499196.21gold quality
right adrenal gland cortexUBERON:003582796.11gold quality
left adrenal glandUBERON:000123496.01gold quality
left adrenal gland cortexUBERON:003582595.91gold quality
hindlimb stylopod muscleUBERON:000425295.90gold quality
right atrium auricular regionUBERON:000663195.83gold quality
adrenal cortexUBERON:000123595.77gold quality
heart right ventricleUBERON:000208095.74gold quality
heartUBERON:000094895.43gold quality
cardiac atriumUBERON:000208195.22gold quality
rectumUBERON:000105295.13gold quality
adrenal glandUBERON:000236995.11gold quality
body of tongueUBERON:001187694.78gold quality
transverse colonUBERON:000115794.58gold quality
right lobe of liverUBERON:000111494.56gold quality
body of pancreasUBERON:000115094.56gold quality
body of stomachUBERON:000116194.54gold quality
muscle of legUBERON:000138394.31gold quality
lower esophagus muscularis layerUBERON:003583394.31gold quality
lower esophagusUBERON:001347394.30gold quality
biceps brachiiUBERON:000150794.17gold quality
gastrocnemiusUBERON:000138894.13gold quality
vena cavaUBERON:000408794.02silver quality
renal medullaUBERON:000036294.01gold quality
muscle layer of sigmoid colonUBERON:003580593.96gold quality
muscle organUBERON:000163093.95gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-MTAB-7606no244.38
E-ANND-3no0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

22 targeting MRPL16, 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-3065-5P99.9771.563281
HSA-MIR-551B-5P99.9671.283493
HSA-MIR-3942-3P99.5769.032854
HSA-MIR-432899.5771.064094
HSA-MIR-3616-5P99.5567.02989
HSA-MIR-57399.5567.44955
HSA-MIR-7159-5P99.5372.122472
HSA-MIR-582-5P99.4770.792635
HSA-MIR-513A-3P99.3970.633620
HSA-MIR-513C-3P99.3970.633620
HSA-MIR-3140-5P99.3969.041136
HSA-MIR-135A-5P99.3671.851601
HSA-MIR-135B-5P99.3671.631613
HSA-MIR-3606-3P99.1169.843254
HSA-MIR-447899.0765.162320
HSA-MIR-222-5P98.7569.171242
HSA-MIR-6868-3P98.6369.642259
HSA-MIR-124898.4767.541314
HSA-MIR-6783-5P97.6767.211528
HSA-MIR-194-3P97.3665.961027
HSA-MIR-444897.0466.22752
HSA-MIR-6734-5P95.7065.56950

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 56.7% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 1)

  • Results from a study on gene expression variability markers in early-stage human embryos shows that MRPL16 is a putative variability and gene expression level marker for the 3-day, 8-cell embryo stage. (PMID:26288249)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriomrpl16ENSDARG00000075325
mus_musculusMrpl16ENSMUSG00000024683
rattus_norvegicusMrpl16ENSRNOG00000021005
drosophila_melanogastermRpL16FBGN0023519
caenorhabditis_elegansWBGENE00011412

Protein

Protein identifiers

Large ribosomal subunit protein uL16mQ9NX20 (reviewed: Q9NX20)

Alternative names: 39S ribosomal protein L16, mitochondrial

All UniProt accessions (2): Q9NX20, E9PI14

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 universal ribosomal protein uL16 family.

RefSeq proteins (1): NP_060310* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000114Ribosomal_uL16_bactFamily
IPR016180Ribosomal_uL16_domDomain
IPR036920Ribosomal_uL16_sfHomologous_superfamily
IPR047873Ribosomal_uL16Family

Pfam: PF00252

UniProt features (26 total): strand 11, helix 7, sequence variant 3, turn 2, transit peptide 1, chain 1, sequence conflict 1

Structure

Experimental structures (PDB)

87 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-Q9NX20-F188.970.83

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: 130 (showing top): GOBP_MITOCHONDRIAL_TRANSLATION, IVANOVA_HEMATOPOIESIS_LATE_PROGENITOR, GOBP_TRANSLATION, GOMF_STRUCTURAL_CONSTITUENT_OF_RIBOSOME, GNF2_FBL, GOCC_MITOCHONDRIAL_ENVELOPE, BERENJENO_TRANSFORMED_BY_RHOA_UP, GOCC_LARGE_RIBOSOMAL_SUBUNIT, GOCC_RIBOSOME, GOCC_ORGANELLAR_RIBOSOME, GOCC_MITOCHONDRIAL_MATRIX, GOCC_ORGANELLE_INNER_MEMBRANE, GOCC_RIBOSOMAL_SUBUNIT, BLALOCK_ALZHEIMERS_DISEASE_DN, GOCC_RIBONUCLEOPROTEIN_COMPLEX

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

GO Molecular Function (2): structural constituent of ribosome (GO:0003735), rRNA binding (GO:0019843)

GO Cellular Component (6): mitochondrion (GO:0005739), mitochondrial inner membrane (GO:0005743), mitochondrial large ribosomal subunit (GO:0005762), ribosome (GO:0005840), large ribosomal subunit (GO:0015934), 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
structural molecule activity1
ribosome1
RNA binding1
cytoplasm1
intracellular membrane-bounded organelle1
organelle inner membrane1
mitochondrial membrane1
organellar large ribosomal subunit1
mitochondrial ribosome1
mitochondrial protein-containing complex1
intracellular membraneless organelle1
ribosomal subunit1
protein-containing complex1

Protein interactions and networks

STRING

4303 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
MRPL16MRPL24Q96A35717
MRPL16MRPL21Q7Z2W9709
MRPL16MRPL17Q9NRX2666
MRPL16MRPL2Q5T653662
MRPL16MRPS16Q9Y3D3595
MRPL16MRPL30Q8TCC3591
MRPL16MRPS11P82912575
MRPL16MRPL11Q9Y3B7561
MRPL16MRPL33O75394552
MRPL16MRPS2Q9Y399551
MRPL16MRPS18CQ9Y3D5534
MRPL16MRPS18AQ9NVS2529
MRPL16MRPL20Q9BYC9522
MRPL16MRPS5P82675507
MRPL16KGD4P82909492

IntAct

179 interactions, top by confidence:

ABTypeScore
YBX1HNRNPRpsi-mi:“MI:0914”(association)0.770
NDUFS3NDUFS8psi-mi:“MI:0914”(association)0.730
MRPL37HSPD1psi-mi:“MI:0914”(association)0.710
CFTRESYT2psi-mi:“MI:2364”(proximity)0.710
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
DHX32POLRMTpsi-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
MRPL28MRPL3psi-mi:“MI:0914”(association)0.530
MRPL41MRPL3psi-mi:“MI:0914”(association)0.530
MRPL16HSPD1psi-mi:“MI:0914”(association)0.530
MRPL2GTPBP10psi-mi:“MI:0914”(association)0.530
MRPL13GTPBP10psi-mi:“MI:0914”(association)0.530
MRPL18GTPBP10psi-mi:“MI:0914”(association)0.530
MRPL16MRPL2psi-mi:“MI:0914”(association)0.530
ABT1ZNF316psi-mi:“MI:0914”(association)0.530
MRPL27MRPL33psi-mi:“MI:0914”(association)0.530
NDUFAB1MIEF1psi-mi:“MI:0915”(physical association)0.490
DDX21MED19psi-mi:“MI:2364”(proximity)0.480

BioGRID (237): MRPL16 (Affinity Capture-MS), HNRNPA1 (Affinity Capture-MS), MRPL16 (Affinity Capture-MS), MRPL16 (Affinity Capture-MS), MRPL16 (Affinity Capture-MS), MRPL16 (Affinity Capture-MS), MRPL16 (Affinity Capture-MS), MRPL16 (Affinity Capture-MS), MRPL16 (Affinity Capture-MS), MRPL16 (Co-fractionation), MRPL16 (Co-fractionation), MRPL16 (Co-fractionation), MRPS7 (Co-fractionation), MRPL16 (Affinity Capture-MS), MRPL16 (Affinity Capture-MS)

ESM2 similar proteins: A0A1D8PDL6, A1CJS8, A1D7P0, A3LQ06, A5DCN7, A5DZE1, A6R3Q6, A6S4J2, A6ZR80, A7TIZ1, O01802, O60143, P05737, P0CQ60, P0CQ61, P0CU36, P11874, P25457, P40078, P60039, P60040, Q0UV95, Q12213, Q1DQ27, Q4P3S7, Q4WX36, Q54GN8, Q54J69, Q5A2Y7, Q5AIB8, Q5B954, Q5M818, Q5R7L3, Q5ZKT8, Q6AZN4, Q6BTA4, Q6BU14, Q6C603, Q6C6D1, Q6CNC5

Diamond homologs: A0ALW1, A0RM18, A0T0I6, A0T0Y0, A1A076, A1W1V3, A2RC21, A3CK70, A4XLS3, A5USI2, A5VLJ8, A6MW08, A6QCQ5, A7H105, A7H649, A7HBM5, A7NR56, A7ZG05, A8AZL8, A8FP14, A8Z675, A9B419, A9KJI7, A9NEE0, A9WH73, B0RZU7, B1I8K5, B1MW07, B2G8X1, B2IS47, B2RLY5, B3DQC1, B4U507, B5E6G2, B5XJ43, B7GND3, B8DB15, B8G6R8, B8ZKG4, B9DSV7

SIGNOR signaling

1 interactions.

AEffectBMechanism
MRPL16“form complex”“39S mitochondrial large ribosomal subunit”binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 161 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 control3737.5×6e-48
Mitochondrial translation3135.2×4e-39
Mitochondrial translation initiation3334.6×2e-41
Mitochondrial translation elongation3334.6×2e-41
Mitochondrial translation termination3329.9×4e-39
Translation3417.4×1e-31
Peptide chain elongation1111.5×1e-07
Viral mRNA Translation1111.5×1e-07

GO biological processes:

GO termPartnersFoldFDR
mitochondrial translation3541.4×2e-45
mitochondrial large ribosomal subunit assembly533.7×4e-05
translation3121.7×2e-30
cytoplasmic translation1215.1×6e-09
negative regulation of translation912.0×1e-05
rRNA processing87.7×1e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance41
Likely benign1
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

523 predictions. Top by Δscore:

VariantEffectΔscore
11:59806829:ATGCC:Aacceptor_loss1.0000
11:59806831:GCC:Gacceptor_loss1.0000
11:59806833:CTAAA:Cacceptor_loss1.0000
11:59807694:CACT:Cdonor_loss1.0000
11:59807695:ACTC:Adonor_loss1.0000
11:59807696:CTCA:Cdonor_loss1.0000
11:59807697:TCA:Tdonor_loss1.0000
11:59807698:CACC:Cdonor_loss1.0000
11:59807699:A:ACdonor_gain1.0000
11:59807699:A:AGdonor_loss1.0000
11:59807700:C:CCdonor_gain1.0000
11:59807700:C:CGdonor_loss1.0000
11:59807847:CAT:Cacceptor_gain1.0000
11:59807849:TCT:Tacceptor_loss1.0000
11:59807850:C:CCacceptor_gain1.0000
11:59807850:CTAAA:Cacceptor_loss1.0000
11:59807851:T:Cacceptor_loss1.0000
11:59809850:CTCA:Cdonor_loss1.0000
11:59809851:TCAC:Tdonor_loss1.0000
11:59809853:A:AGdonor_loss1.0000
11:59809854:CCTTC:Cdonor_loss1.0000
11:59809918:AATC:Aacceptor_loss1.0000
11:59809919:ATC:Aacceptor_loss1.0000
11:59809920:TCTA:Tacceptor_loss1.0000
11:59809921:C:CCacceptor_gain1.0000
11:59809921:CT:Cacceptor_loss1.0000
11:59806830:TGC:Tacceptor_gain0.9900
11:59806833:C:CCacceptor_gain0.9900
11:59806834:T:Aacceptor_loss0.9900
11:59806839:G:Cacceptor_gain0.9900

AlphaMissense

1645 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
11:59806739:A:GW122R0.989
11:59806739:A:TW122R0.989
11:59806746:A:CF119L0.984
11:59806746:A:TF119L0.984
11:59806748:A:GF119L0.984
11:59806716:C:AK129N0.983
11:59806716:C:GK129N0.983
11:59806786:C:GR106P0.983
11:59807705:A:TI89N0.979
11:59807708:G:TA88E0.977
11:59806744:G:TA120D0.975
11:59806771:C:GR111P0.975
11:59806466:A:GW213R0.974
11:59806466:A:TW213R0.974
11:59806642:A:TV154E0.974
11:59806787:G:TR106S0.973
11:59806543:G:TA187E0.971
11:59806548:G:CF185L0.968
11:59806548:G:TF185L0.968
11:59806550:A:GF185L0.968
11:59806470:G:CN211K0.967
11:59806470:G:TN211K0.967
11:59806831:G:TA91E0.966
11:59806624:A:TV160D0.965
11:59807753:C:GR73P0.965
11:59807705:A:GI89T0.964
11:59807709:C:GA88P0.964
11:59807726:A:GF82S0.964
11:59806630:C:GR158P0.963
11:59806813:A:GL97P0.962

dbSNP variants (sampled 300 via entrez): RS1000040802 (11:59809292 C>T), RS1000207020 (11:59805730 C>A), RS1000661079 (11:59807372 A>G), RS1000730486 (11:59806013 G>A), RS1000948304 (11:59807027 C>T), RS1001936686 (11:59806478 T>C,G), RS1002041672 (11:59812334 T>G), RS1002237202 (11:59809643 C>A), RS1002561490 (11:59807965 G>A), RS1003457207 (11:59806093 A>G), RS1004030231 (11:59807587 G>A,T), RS1004347763 (11:59812455 G>A), RS1004392815 (11:59806118 G>A,T), RS1004709835 (11:59807483 C>G,T), RS1005582911 (11:59812400 G>A)

Disease associations

OMIM: gene MIM:611829 | 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

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

ChemicalActions (top 5)PubMed papers
Acetaminophenaffects cotreatment, decreases expression4
sodium arseniteincreases expression, decreases expression2
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxidedecreases expression2
Cyclosporinedecreases expression2
aristolochic acid Idecreases expression1
triphenyl phosphateaffects expression1
arseniteaffects binding, increases reaction1
tris(1,3-dichloro-2-propyl)phosphatedecreases expression1
potassium chromate(VI)affects cotreatment, decreases expression1
epigallocatechin gallateaffects cotreatment, decreases expression1
corosolic aciddecreases expression1
K 7174decreases expression1
bisphenol Bincreases expression1
abrinedecreases expression1
Grape Seed Proanthocyanidinsaffects cotreatment, decreases expression1
NSC 689534affects binding, decreases expression1
bisphenol AFincreases expression1
Resveratrolaffects cotreatment, increases expression1
Air Pollutantsdecreases expression, increases abundance1
Arsenicaffects methylation1
Benzo(a)pyreneincreases methylation1
Carbamazepineaffects expression1
Catechinaffects cotreatment, decreases expression1
Copperaffects binding, decreases expression1
Dimethyl Sulfoxideincreases expression1
Drugs, Chinese Herbaldecreases expression1
Lipopolysaccharidesaffects cotreatment, decreases expression1
Piroxicamdecreases expression1
Plant Extractsaffects cotreatment, increases expression1
Ribonucleotidesaffects binding1

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.