MRPL47

gene
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Also known as CGI-204NCM1uL29m

Summary

MRPL47 (mitochondrial ribosomal protein L47, HGNC:16652) is a protein-coding gene on chromosome 3q26.33, encoding Large ribosomal subunit protein uL29m (Q9HD33). It is a selective cancer dependency (DepMap: 22.9% 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. This gene is immediately adjacent to the gene for BAF complex 53 kDa subunit protein a (BAF53a), in a tail-to-tail orientation. Two transcript variants encoding different protein isoforms have been identified.

Source: NCBI Gene 57129 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 48 total
  • Cancer dependency (DepMap): dependent in 22.9% of screened cell lines
  • MANE Select transcript: NM_020409

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:16652
Approved symbolMRPL47
Namemitochondrial ribosomal protein L47
Location3q26.33
Locus typegene with protein product
StatusApproved
AliasesCGI-204, NCM1, uL29m
Ensembl geneENSG00000136522
Ensembl biotypeprotein_coding
OMIM611852
Entrez57129

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 5 protein_coding

ENST00000259038, ENST00000392659, ENST00000476781, ENST00000937961, ENST00000937962

RefSeq mRNA: 2 — MANE Select: NM_020409 NM_020409, NM_177988

CCDS: CCDS3232, CCDS3233

Canonical transcript exons

ENST00000476781 — 7 exons

ExonStartEnd
ENSE00000924284179592644179592739
ENSE00000924285179593765179593895
ENSE00001870688179604527179604638
ENSE00001921076179588285179588995
ENSE00002285161179602652179602797
ENSE00003498247179601730179601790
ENSE00003510817179598675179598771

Expression profiles

Bgee: expression breadth ubiquitous, 260 present calls, max score 98.48.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 36.5464 / max 664.7939, expressed in 1810 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
4572832.39561807
457294.15081578

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
left ventricle myocardiumUBERON:000656698.48gold quality
tibialis anteriorUBERON:000138598.00gold quality
myocardiumUBERON:000234997.78gold quality
heart right ventricleUBERON:000208097.34gold quality
cardiac muscle of right atriumUBERON:000337996.98gold quality
ileal mucosaUBERON:000033196.58gold quality
deltoidUBERON:000147696.56gold quality
upper arm skinUBERON:000426396.31gold quality
kidney epitheliumUBERON:000481996.03gold quality
nasal cavity epitheliumUBERON:000538495.78gold quality
quadriceps femorisUBERON:000137795.74gold quality
gingival epitheliumUBERON:000194995.48gold quality
vastus lateralisUBERON:000137995.47gold quality
mucosa of sigmoid colonUBERON:000499395.22gold quality
vena cavaUBERON:000408795.16gold quality
biceps brachiiUBERON:000150795.09gold quality
colonic mucosaUBERON:000031795.02gold quality
gingivaUBERON:000182895.02gold quality
body of tongueUBERON:001187694.96gold quality
adrenal tissueUBERON:001830394.89gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450294.85gold quality
islet of LangerhansUBERON:000000694.83gold quality
spermCL:000001994.80gold quality
adult organismUBERON:000702394.80gold quality
epithelial cell of pancreasCL:000008394.66gold quality
oral cavityUBERON:000016794.36gold quality
skeletal muscle tissueUBERON:000113494.36gold quality
muscle tissueUBERON:000238594.23gold quality
pharyngeal mucosaUBERON:000035594.19gold quality
left testisUBERON:000453394.06gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes7.94

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

22 targeting MRPL47, 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-340-5P100.0072.504437
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-196A-1-3P99.9972.152772
HSA-MIR-4699-3P99.7170.153142
HSA-MIR-497-3P99.6169.711990
HSA-MIR-486-5P99.5170.39707
HSA-MIR-377-3P99.3770.181905
HSA-MIR-6507-3P99.3567.321059
HSA-MIR-1211399.3267.541072
HSA-MIR-877-3P99.0968.101637
HSA-MIR-4796-3P99.0868.381681
HSA-MIR-224-3P98.9168.421815
HSA-MIR-522-3P98.9168.561817
HSA-MIR-453998.7867.18888
HSA-MIR-513B-3P98.7668.121577
HSA-MIR-216B-3P98.5567.191223
HSA-MIR-3144-3P98.1567.34677
HSA-MIR-425797.8668.051190
HSA-MIR-366597.7365.08975
HSA-MIR-59697.4863.13469
HSA-MIR-875-5P96.7466.48579
HSA-MIR-103B95.5166.85441

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 22.9% of screened cell lines.

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriomrpl47ENSDARG00000075743
mus_musculusMrpl47ENSMUSG00000037531
rattus_norvegicusMrpl47ENSRNOG00000011639
drosophila_melanogastermRpL47FBGN0014023
caenorhabditis_elegansmrpl-47WBGENE00015092

Protein

Protein identifiers

Large ribosomal subunit protein uL29mQ9HD33 (reviewed: Q9HD33)

Alternative names: 39S ribosomal protein L47, mitochondrial, Nasopharyngeal carcinoma metastasis-related protein 1

All UniProt accessions (1): Q9HD33

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 uL29 family.

Isoforms (3)

UniProt IDNamesCanonical?
Q9HD33-11yes
Q9HD33-22
Q9HD33-33

RefSeq proteins (2): NP_065142, NP_817125 (=MANE)

Domains & families (InterPro)

IDNameType
IPR010729Ribosomal_uL29_mitFamily
IPR038340MRP-L47_sfHomologous_superfamily

Pfam: PF06984

UniProt features (22 total): helix 8, strand 5, splice variant 2, sequence variant 2, transit peptide 1, chain 1, turn 1, modified residue 1, sequence conflict 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-Q9HD33-F184.040.72

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): 144

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: 116 (showing top): RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP, MODULE_255, GOBP_MITOCHONDRIAL_TRANSLATION, MODULE_317, TGACCTY_ERR1_Q2, chr3q26, GOBP_TRANSLATION, WEI_MYCN_TARGETS_WITH_E_BOX, MILI_PSEUDOPODIA_HAPTOTAXIS_UP, GOMF_STRUCTURAL_CONSTITUENT_OF_RIBOSOME, GOCC_MITOCHONDRIAL_ENVELOPE, AACTTT_UNKNOWN, DING_LUNG_CANCER_EXPRESSION_BY_COPY_NUMBER, FOXJ2_02

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

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

GO Cellular Component (6): mitochondrion (GO:0005739), mitochondrial inner membrane (GO:0005743), mitochondrial large ribosomal subunit (GO:0005762), mitochondrial ribosome (GO:0005761), 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
structural molecule activity1
ribosome1
cytoplasm1
intracellular membrane-bounded organelle1
organelle inner membrane1
mitochondrial membrane1
organellar large ribosomal subunit1
mitochondrial ribosome1
mitochondrial protein-containing complex1
organellar ribosome1
mitochondrial matrix1
intracellular membraneless organelle1
protein-containing complex1

Protein interactions and networks

STRING

2684 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
MRPL47MRPL9Q9BYD2661
MRPL47MRPS33Q9Y291644
MRPL47CHCHD1Q96BP2625
MRPL47MRPL4Q9BYD3623
MRPL47MRPL20Q9BYC9619
MRPL47MRPL23Q16540606
MRPL47MRPL12P52815587
MRPL47MRPL33O75394529
MRPL47MRPS18BQ9Y676512
MRPL47MRPL42Q9Y6G3494
MRPL47MRPL53Q96EL3491
MRPL47MRPS5P82675491
MRPL47MRPL36Q9P0J6488
MRPL47MRPL54Q6P161486
MRPL47MRPL50Q8N5N7483

IntAct

131 interactions, top by confidence:

ABTypeScore
MRPL37HSPD1psi-mi:“MI:0914”(association)0.710
MRPS30GTPBP10psi-mi:“MI:0914”(association)0.640
LIN28AIGF2BP3psi-mi:“MI:0914”(association)0.640
NPKPNA6psi-mi:“MI:0914”(association)0.550
HSPD1MRPL47psi-mi:“MI:0915”(physical association)0.540
MRPL50GTPBP10psi-mi:“MI:0914”(association)0.530
MRPL2GTPBP10psi-mi:“MI:0914”(association)0.530
ZNF324BZNF316psi-mi:“MI:0914”(association)0.530
PDGFBDKC1psi-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
MRPL23BCKDHApsi-mi:“MI:0914”(association)0.530
MRPL27MRPL33psi-mi:“MI:0914”(association)0.530
NDUFAB1MIEF1psi-mi:“MI:0915”(physical association)0.490
MRPL47PDIA3psi-mi:“MI:0915”(physical association)0.400
Ybx1MRPS18Bpsi-mi:“MI:0915”(physical association)0.400
NPKPNA6psi-mi:“MI:0914”(association)0.350
NPTRIM66psi-mi:“MI:0914”(association)0.350
psi-mi:“MI:0914”(association)0.350
ESR1ESYT2psi-mi:“MI:0914”(association)0.350
LRRK2psi-mi:“MI:0914”(association)0.350
ATAD3BGTPBP10psi-mi:“MI:0914”(association)0.350

BioGRID (373): MRPL47 (Affinity Capture-MS), MRPL47 (Affinity Capture-MS), MRPL47 (Affinity Capture-MS), MRPL47 (Affinity Capture-MS), MRPL47 (Affinity Capture-MS), MRPL47 (Affinity Capture-MS), MRPL47 (Affinity Capture-MS), MRPL47 (Affinity Capture-MS), MRPL47 (Affinity Capture-MS), MRPL47 (Affinity Capture-MS), MRPL47 (Affinity Capture-MS), MRPL47 (Affinity Capture-MS), MRPL12 (Affinity Capture-MS), MRPL45 (Affinity Capture-MS), MRPL46 (Affinity Capture-MS)

ESM2 similar proteins: A1C6F8, A1DH31, A1Z897, A2QCC7, A3KP74, A4RHR8, A6RDX3, A6SLT9, A7EWR0, B0XK69, B3MI37, B3N6D9, B3N8S9, B4GDB3, B4GG58, B4HMQ1, B4HRL4, B4KN44, B4KPG8, B4LKE5, B4MRE7, B4N665, B4NXN5, B4P2P8, B4QFP7, B4QID8, B5DZ31, B5E0U2, P0CR32, P0CR33, P36527, P87232, Q08DT6, Q0CXX1, Q0U6J9, Q178L7, Q1DNY5, Q1K5G1, Q1K6U7, Q2H080

Diamond homologs: A1C6F8, A1DH31, A2QCC7, A3LYY9, A4RHR8, A5DH98, A5E713, A6RDX3, A6SLT9, A7A1V9, A7EWR0, A7TNQ2, P36517, P87232, Q08DT6, Q0CXX1, Q0U6J9, Q1DNY5, Q2H080, Q4X156, Q59RP7, Q5B0N3, Q6BQK3, Q6CF20, Q6CWC4, Q6FK61, Q756Y8, Q7S910, Q8K2Y7, Q9HD33

SIGNOR signaling

1 interactions.

AEffectBMechanism
MRPL47“form complex”“39S mitochondrial large ribosomal subunit”binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 130 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 control3340.5×2e-43
Mitochondrial translation2939.9×3e-38
Mitochondrial translation initiation3139.3×1e-40
Mitochondrial translation elongation3139.3×1e-40
Mitochondrial translation termination3134.0×2e-38
Translation3219.9×1e-31
Peptide chain elongation911.4×4e-06
Viral mRNA Translation911.4×4e-06

GO biological processes:

GO termPartnersFoldFDR
mitochondrial translation3146.4×1e-41
translation2623.0×6e-26
cytoplasmic translation1016.0×2e-07
negative regulation of translation711.8×4e-04
ribosomal small subunit biogenesis611.8×1e-03
regulation of alternative mRNA splicing, via spliceosome510.5×9e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance39
Likely benign1
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1351 predictions. Top by Δscore:

VariantEffectΔscore
3:179583348:CCTA:Cacceptor_loss1.0000
3:179583349:CTAG:Cacceptor_loss1.0000
3:179583350:TAG:Tacceptor_loss1.0000
3:179583351:A:AGacceptor_gain1.0000
3:179583351:AG:Aacceptor_gain1.0000
3:179583351:AGGGT:Aacceptor_loss1.0000
3:179583352:G:GGacceptor_gain1.0000
3:179583352:GG:Gacceptor_gain1.0000
3:179583352:GGGT:Gacceptor_gain1.0000
3:179583444:CTCCA:Cdonor_gain1.0000
3:179583445:TCCA:Tdonor_gain1.0000
3:179583446:CCA:Cdonor_gain1.0000
3:179583447:CA:Cdonor_gain1.0000
3:179583448:AG:Adonor_loss1.0000
3:179583449:G:GGdonor_gain1.0000
3:179583450:TA:Tdonor_loss1.0000
3:179583451:AA:Adonor_loss1.0000
3:179586448:G:GTdonor_gain1.0000
3:179586544:A:AGacceptor_gain1.0000
3:179586545:G:GGacceptor_gain1.0000
3:179586545:GA:Gacceptor_gain1.0000
3:179586545:GAGT:Gacceptor_gain1.0000
3:179587926:ACAG:Aacceptor_gain1.0000
3:179587928:AG:Aacceptor_gain1.0000
3:179587929:GG:Gacceptor_gain1.0000
3:179588996:C:CCacceptor_gain1.0000
3:179593761:ATAC:Adonor_loss1.0000
3:179593762:TACC:Tdonor_loss1.0000
3:179593763:A:ACdonor_gain1.0000
3:179593763:A:AGdonor_loss1.0000

AlphaMissense

1624 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
3:179601782:A:GW85R0.995
3:179601782:A:TW85R0.995
3:179593851:T:AR149S0.993
3:179593851:T:GR149S0.993
3:179601756:T:AK93N0.993
3:179601756:T:GK93N0.993
3:179598756:T:AK107N0.992
3:179598756:T:GK107N0.992
3:179601780:C:AW85C0.992
3:179601780:C:GW85C0.992
3:179593844:C:GA152P0.991
3:179598693:A:CS128R0.991
3:179598693:A:TS128R0.991
3:179598695:T:GS128R0.991
3:179598722:C:GA119P0.990
3:179598760:A:GL106P0.990
3:179601766:A:GL90P0.990
3:179593886:A:GS138P0.988
3:179598747:G:CN110K0.988
3:179598747:G:TN110K0.988
3:179601731:A:GW102R0.988
3:179601731:A:TW102R0.988
3:179593885:G:AS138F0.986
3:179598733:A:GL115P0.986
3:179598742:A:GL112P0.986
3:179601762:C:AR91S0.986
3:179601762:C:GR91S0.986
3:179602695:A:CF67L0.986
3:179602695:A:TF67L0.986
3:179602697:A:GF67L0.986

dbSNP variants (sampled 300 via entrez): RS1000484349 (3:179596553 C>T), RS1000577197 (3:179599666 G>T), RS1000631110 (3:179592423 T>C), RS1000642297 (3:179605703 A>G), RS1000732963 (3:179605335 AAGACAGGTAATATGT>A), RS1000869720 (3:179591543 T>C), RS1000902589 (3:179587815 A>G), RS1001077561 (3:179598098 C>T), RS1001210667 (3:179605477 GT>G), RS1001226889 (3:179604176 A>T), RS1001290658 (3:179603727 C>A,T), RS1001530382 (3:179597733 G>A,C), RS1001634194 (3:179593312 C>G), RS1001861685 (3:179606162 C>T), RS1001876677 (3:179592941 G>A)

Disease associations

OMIM: gene MIM:611852 | 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)

PharmGKB variants

1 variants.

VariantGenesLevelScore#Clin annotsDrugs
rs10513762MRPL470.000

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
bisphenol Saffects expression, increases expression2
Tobacco Smoke Pollutionincreases expression2
dicrotophosdecreases expression1
bisphenol Adecreases expression1
arseniteaffects binding, increases reaction1
mono-(2-ethylhexyl)phthalatedecreases expression1
sodium arseniteincreases abundance, increases expression1
gossypol acetic aciddecreases expression1
cylindrospermopsinincreases expression1
CGP 52608affects binding, increases reaction1
corosolic aciddecreases expression1
ICG 001decreases expression1
abrineincreases expression1
Resveratrolaffects cotreatment, decreases expression, increases expression1
Acetaminophenaffects cotreatment, decreases expression1
Arsenicincreases abundance, increases expression1
Diurondecreases expression1
Ivermectindecreases expression1
Leadaffects expression1
Lipopolysaccharidesaffects cotreatment, decreases expression1
Oligomycinsaffects response to substance, increases expression1
Plant Extractsaffects cotreatment, decreases expression, increases expression1
Quercetindecreases expression1
Ribonucleotidesaffects binding1
Rotenonedecreases expression1
Urethanedecreases expression1
Lithium Chloridedecreases expression1
Lactic Aciddecreases expression1
Acrylamideincreases expression1
Particulate Matterdecreases 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.