MRM3

gene
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Also known as FLJ10581HC90RMTL1

Summary

MRM3 (mitochondrial rRNA methyltransferase 3, HGNC:18485) is a protein-coding gene on chromosome 17p13.3, encoding rRNA methyltransferase 3, mitochondrial (Q9HC36). S-adenosyl-L-methionine-dependent 2’-O-ribose methyltransferase that catalyzes the formation of 2’-O-methylguanosine at position 1370 (Gm1370) in the 16S mitochondrial large subunit ribosomal RNA (mtLSU rRNA), a conserved modification in the peptidyl transferase domain of the mt…. It is a selective cancer dependency (DepMap: 11.6% of cell lines).

Efficient translation of mitochondrial-derived transcripts requires proper assembly of the large subunit of the mitochondrial ribosome. Central to the biogenesis of this large subunit is the A-loop of mitochondrial 16S rRNA, which is modified by three rRNA methyltransferases located near mtDNA nucleoids. The protein encoded by this gene methylates G(1370) of 16S rRNA, and this modification is necessary for proper ribosomal large subnit assembly. Two transcript variants encoding different isoforms have been found for this gene.

Source: NCBI Gene 55178 — RefSeq curated summary.

At a glance

  • GWAS associations: 1
  • Clinical variants (ClinVar): 12 total
  • Cancer dependency (DepMap): dependent in 11.6% of screened cell lines
  • MANE Select transcript: NM_018146

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:18485
Approved symbolMRM3
Namemitochondrial rRNA methyltransferase 3
Location17p13.3
Locus typegene with protein product
StatusApproved
AliasesFLJ10581, HC90, RMTL1
Ensembl geneENSG00000171861
Ensembl biotypeprotein_coding
OMIM612600
Entrez55178

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 6 protein_coding, 1 nonsense_mediated_decay, 1 retained_intron

ENST00000304478, ENST00000571157, ENST00000574509, ENST00000574916, ENST00000872466, ENST00000872467, ENST00000938389, ENST00000938390

RefSeq mRNA: 2 — MANE Select: NM_018146 NM_001317947, NM_018146

CCDS: CCDS10997

Canonical transcript exons

ENST00000304478 — 4 exons

ExonStartEnd
ENSE00001130996783083783327
ENSE00001199338782353782692
ENSE00001265741791534792509
ENSE00003507601787965788132

Expression profiles

Bgee: expression breadth ubiquitous, 263 present calls, max score 92.31.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 14.9915 / max 124.8042, expressed in 1810 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
15869114.85471810
1586920.136856

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
endothelial cellCL:000011592.31gold quality
gastrocnemiusUBERON:000138889.93gold quality
muscle of legUBERON:000138389.37gold quality
apex of heartUBERON:000209888.67gold quality
hindlimb stylopod muscleUBERON:000425287.76gold quality
muscle organUBERON:000163087.27gold quality
gluteal muscleUBERON:000200087.00gold quality
gingival epitheliumUBERON:000194986.78gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099186.73gold quality
body of pancreasUBERON:000115086.55gold quality
spermCL:000001986.37gold quality
deltoidUBERON:000147685.67silver quality
right lobe of liverUBERON:000111485.63gold quality
heart left ventricleUBERON:000208485.38gold quality
cardiac ventricleUBERON:000208285.06gold quality
mucosa of transverse colonUBERON:000499185.00gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047384.79gold quality
left testisUBERON:000453384.54gold quality
pancreasUBERON:000126484.44gold quality
right adrenal glandUBERON:000123384.29gold quality
right adrenal gland cortexUBERON:003582784.29gold quality
testisUBERON:000047384.23gold quality
body of stomachUBERON:000116184.23gold quality
male germ cellCL:000001584.21gold quality
right testisUBERON:000453484.15gold quality
left adrenal glandUBERON:000123483.98gold quality
gingivaUBERON:000182883.92gold quality
cervix squamous epitheliumUBERON:000692283.90gold quality
skin of legUBERON:000151183.87gold quality
lower esophagus muscularis layerUBERON:003583383.84gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes3.72

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): CREB1

miRNA regulators (miRDB)

20 targeting MRM3, 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-6778-3P99.9667.292693
HSA-MIR-806399.9169.763146
HSA-MIR-1211999.8768.351653
HSA-MIR-6752-3P99.7266.711587
HSA-MIR-7152-5P99.6069.332094
HSA-MIR-427699.5667.662514
HSA-MIR-2116-5P99.3269.341273
HSA-MIR-797499.2465.481137
HSA-MIR-767-3P98.6167.691192
HSA-MIR-138-5P98.4370.491292
HSA-MIR-313898.4167.53744
HSA-MIR-3187-5P98.3665.741776
HSA-MIR-660-3P98.1466.041434
HSA-MIR-1285-3P97.7267.021932
HSA-MIR-5189-5P97.7266.961814
HSA-MIR-61297.2665.951597
HSA-MIR-686097.2166.311656
HSA-MIR-807195.6964.93484
HSA-MIR-476593.1166.17737
HSA-MIR-805392.8266.1279

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 11.6% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 3)

  • The ATF/CREB site is the key element for transcription of this protein found on human chromosome 17. (PMID:12296377)
  • MRM2 and MRM3 are human mitochondrial methyltransferases involved in the modification of 16S rRNA and are important factors for the biogenesis and function of the large subunit of the mitochondrial ribosome. (PMID:25009282)
  • Data show that 2’-O-methyltransferases MRM1, MRM2, and RNMTL1 are responsible for modification of large subunit rRNA at residues G1145, U1369, and G1370, respectively. (PMID:25074936)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
mus_musculusMrm3ENSMUSG00000038046
rattus_norvegicusMrm3ENSRNOG00000037238
caenorhabditis_elegansWBGENE00020498

Paralogs (2): TARBP1 (ENSG00000059588), MRM1 (ENSG00000278619)

Protein

Protein identifiers

rRNA methyltransferase 3, mitochondrialQ9HC36 (reviewed: Q9HC36)

Alternative names: 16S rRNA (guanosine(1370)-2’-O)-methyltransferase, 16S rRNA [Gm1370] 2’-O-methyltransferase, RNA methyltransferase-like protein 1

All UniProt accessions (3): Q9HC36, I3L0T6, I3L443

UniProt curated annotations — full annotation on UniProt →

Function. S-adenosyl-L-methionine-dependent 2’-O-ribose methyltransferase that catalyzes the formation of 2’-O-methylguanosine at position 1370 (Gm1370) in the 16S mitochondrial large subunit ribosomal RNA (mtLSU rRNA), a conserved modification in the peptidyl transferase domain of the mtLSU rRNA. Also required for formation of 2’-O-methyluridine at position 1369 (Um1369) mediated by MRM2.

Subcellular location. Mitochondrion.

Tissue specificity. Expressed at same level in normal liver and hepatocarcinoma.

Similarity. Belongs to the class IV-like SAM-binding methyltransferase superfamily. RNA methyltransferase TrmH family.

RefSeq proteins (2): NP_001304876, NP_060616* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001537SpoU_MeTrfaseDomain
IPR013123SpoU_subst-bdDomain
IPR029026tRNA_m1G_MTases_NHomologous_superfamily
IPR029028Alpha/beta_knot_MTasesHomologous_superfamily
IPR029064Ribosomal_eL30-like_sfHomologous_superfamily
IPR051259rRNA_MethyltransferaseFamily
IPR053888MRM3-like_sub_bindDomain

Pfam: PF00588, PF22435

Enzyme classification (BRENDA):

  • EC 2.1.1.B124 — (BRENDA: organisms, substrates, inhibitors, Km, kcat entries)

Catalyzed reactions (Rhea), 1 shown:

  • guanosine(1370) in 16S rRNA + S-adenosyl-L-methionine = 2’-O-methylguanosine(1370) in 16S rRNA + S-adenosyl-L-homocysteine + H(+) (RHEA:47756)

UniProt features (12 total): sequence variant 4, binding site 3, transit peptide 1, chain 1, sequence conflict 1, region of interest 1, compositionally biased region 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
7OI6ELECTRON MICROSCOPY5.7

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9HC36-F174.540.51

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Ligand- & substrate-binding residues (3): 356; 380; 389

Function

Pathways and Gene Ontology

Reactome pathways

4 pathways

IDPathway
R-HSA-6793080rRNA modification in the mitochondrion
R-HSA-72312rRNA processing
R-HSA-8868766rRNA processing in the mitochondrion
R-HSA-8953854Metabolism of RNA

MSigDB gene sets: 151 (showing top): GOBP_RIBOSOME_BIOGENESIS, GOBP_RIBOSOME_ASSEMBLY, GOBP_RNA_METHYLATION, MUELLER_PLURINET, GOBP_RNA_MODIFICATION, GOBP_RIBOSOMAL_LARGE_SUBUNIT_ASSEMBLY, BLALOCK_ALZHEIMERS_DISEASE_UP, E4F1_Q6, GOBP_PROTEIN_RNA_COMPLEX_ORGANIZATION, GOBP_ORGANELLE_ASSEMBLY, MCCLUNG_COCAINE_REWARD_5D, RICKMAN_TUMOR_DIFFERENTIATED_MODERATELY_VS_POORLY_UP, GOBP_RRNA_MODIFICATION, GOBP_METHYLATION, GOBP_RIBONUCLEOPROTEIN_COMPLEX_BIOGENESIS

GO Biological Process (5): rRNA 2’-O-methylation (GO:0000451), rRNA processing (GO:0006364), mitochondrial large ribosomal subunit assembly (GO:1902775), RNA processing (GO:0006396), methylation (GO:0032259)

GO Molecular Function (7): RNA binding (GO:0003723), identical protein binding (GO:0042802), rRNA (guanosine-2’-O-ribose)-methyltransferase activity (GO:0070039), protein binding (GO:0005515), methyltransferase activity (GO:0008168), RNA methyltransferase activity (GO:0008173), transferase activity (GO:0016740)

GO Cellular Component (3): mitochondrion (GO:0005739), mitochondrial matrix (GO:0005759), cytoplasm (GO:0005737)

Reactome top-level categories

Rollup of top-3 pathways:

CategoryPathways
rRNA processing in the mitochondrion1
Metabolism of RNA1
rRNA processing1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
rRNA methylation1
RNA processing1
rRNA metabolic process1
ribosome biogenesis1
ribosomal large subunit assembly1
mitochondrial ribosome assembly1
gene expression1
RNA biosynthetic process1
primary metabolic process1
metabolic process1
nucleic acid binding1
protein binding1
rRNA 2’-O-methylation1
rRNA (guanine) methyltransferase activity1
RNA 2’-O-methyltransferase activity1
binding1
transferase activity, transferring one-carbon groups1
methyltransferase activity1
catalytic activity, acting on RNA1
catalytic activity1
cytoplasm1
intracellular membrane-bounded organelle1
mitochondrion1
intracellular organelle lumen1
intracellular anatomical structure1
cellular anatomical structure1

Protein interactions and networks

STRING

2159 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
MRM3MRM2Q9UI43830
MRM3MRM1Q6IN84807
MRM3DDX28Q9NUL7802
MRM3MALSU1Q96EH3761
MRM3MTERF3Q96E29752
MRM3NSUN4Q96CB9710
MRM3RPUSD4Q96CM3701
MRM3METTL15A6NJ78693
MRM3METTL1Q9UBP6685
MRM3NGRNQ9NPE2676
MRM3GTPBP10A4D1E9661
MRM3FASTKD2Q9NYY8654
MRM3MTERF4Q7Z6M4652
MRM3MTG2Q9H4K7650
MRM3TFB1MQ8WVM0630

IntAct

169 interactions, top by confidence:

ABTypeScore
NMRM3psi-mi:“MI:0915”(physical association)0.770
NHNRNPRpsi-mi:“MI:0914”(association)0.730
FHL3MRM3psi-mi:“MI:0915”(physical association)0.720
CFTRESYT2psi-mi:“MI:2364”(proximity)0.710
MRPS30GTPBP10psi-mi:“MI:0914”(association)0.640
SCARF1MRM3psi-mi:“MI:0915”(physical association)0.560
TNFMRM3psi-mi:“MI:0915”(physical association)0.560
MIPMRM3psi-mi:“MI:0915”(physical association)0.560
MRM3AIG1psi-mi:“MI:0915”(physical association)0.560
BTN2A2MRM3psi-mi:“MI:0915”(physical association)0.560
MRM3MRM3psi-mi:“MI:0915”(physical association)0.560
GAD2MRM3psi-mi:“MI:0915”(physical association)0.560
ARLNMRM3psi-mi:“MI:0915”(physical association)0.560
ZFPL1MRM3psi-mi:“MI:0915”(physical association)0.560
JAGN1MRM3psi-mi:“MI:0915”(physical association)0.560
GALNT2MRM3psi-mi:“MI:0915”(physical association)0.560
MRM3UBIAD1psi-mi:“MI:0915”(physical association)0.560
MRPL50GTPBP10psi-mi:“MI:0914”(association)0.530
ZNF512ZNF724psi-mi:“MI:0914”(association)0.530
MRPL42GATCpsi-mi:“MI:0914”(association)0.530
MRM3NDUFS6psi-mi:“MI:0914”(association)0.530
MRPL28MRPL3psi-mi:“MI:0914”(association)0.530
NHNRNPDLpsi-mi:“MI:0914”(association)0.530

BioGRID (223): RNMTL1 (Two-hybrid), RNMTL1 (Affinity Capture-MS), RNMTL1 (Affinity Capture-MS), RNMTL1 (Affinity Capture-MS), RNMTL1 (Affinity Capture-MS), RNMTL1 (Affinity Capture-MS), RNMTL1 (Affinity Capture-MS), PMPCB (Affinity Capture-MS), SPTY2D1 (Affinity Capture-MS), RNMTL1 (Affinity Capture-MS), RNMTL1 (Affinity Capture-MS), RNMTL1 (Reconstituted Complex), RNMTL1 (Affinity Capture-MS), RNMTL1 (Affinity Capture-MS), RNMTL1 (Affinity Capture-MS)

ESM2 similar proteins: A0JPF9, A4D126, A5PKL6, A6QP81, B2GUS6, D2H8V8, E1BCH6, E1BVR9, E9PYK3, F1ND48, G5E8F4, P79106, Q28CZ7, Q32PY6, Q3U269, Q3U3W5, Q3U5Q7, Q3UVV9, Q49MI3, Q4R3W5, Q5F3V0, Q5ND52, Q5R5X9, Q5RCP1, Q5RFM7, Q5RJG7, Q5RL51, Q5S6T3, Q5T8I9, Q5VZV1, Q6AYG3, Q8BIW1, Q8BK58, Q8BQJ6, Q8BTK5, Q8BZ20, Q8C5V5, Q8CAE2, Q8IXQ6, Q8IYR2

Diamond homologs: A1L2E4, A4QNL8, P94538, Q566V3, Q5ND52, Q5SM16, Q6GPJ4, Q72GI1, Q7VQP0, Q9HC36, Q9VW14, A0R557, A1TG08, A1UMF4, A3Q6V9, A4T5L0, D7A3L6, O30272, O51081, O51468, O67577, P0AGJ2, P0AGJ3, P0AGJ4, P44906, P47494, P52393, P63177, P63178, P63179, P63180, P75424, Q06753, Q1B2P4, Q49V41, Q6D127, Q6FF50, Q6LM40, Q7MH13, Q7MYU6

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 151 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 control2023.6×6e-20
Mitochondrial translation1722.5×7e-17
Mitochondrial translation initiation1822.0×1e-17
Mitochondrial translation elongation1822.0×1e-17
Mitochondrial translation termination1819.0×1e-16
Translation2011.9×1e-14
rRNA modification in the nucleus and cytosol59.0×3e-03
Peptide chain elongation78.5×6e-04

GO biological processes:

GO termPartnersFoldFDR
mitochondrial translation2126.4×1e-21
cytoplasmic translation810.7×2e-04
translation1410.4×3e-08
ribosomal small subunit biogenesis69.9×4e-03
RNA processing69.5×5e-03
rRNA processing88.2×1e-03
RNA splicing106.4×8e-04
mRNA processing95.1×7e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance6
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

484 predictions. Top by Δscore:

VariantEffectΔscore
17:782640:G:GTdonor_gain1.0000
17:782640:G:Tdonor_gain1.0000
17:783082:GCAGT:Gacceptor_gain1.0000
17:791526:T:Gacceptor_gain1.0000
17:791528:TTCCA:Tacceptor_loss1.0000
17:791529:TCCA:Tacceptor_loss1.0000
17:791530:CCA:Cacceptor_loss1.0000
17:791531:CAG:Cacceptor_loss1.0000
17:791532:A:AGacceptor_gain1.0000
17:791533:G:GAacceptor_loss1.0000
17:791533:G:GGacceptor_gain1.0000
17:791533:GGCT:Gacceptor_gain1.0000
17:782684:GAGGC:Gdonor_gain0.9900
17:782687:GC:Gdonor_gain0.9900
17:783082:GCA:Gacceptor_gain0.9900
17:783319:GAA:Gdonor_gain0.9900
17:791525:A:AGacceptor_gain0.9900
17:791532:AG:Aacceptor_gain0.9900
17:791532:AGGCT:Aacceptor_gain0.9900
17:791533:GG:Gacceptor_gain0.9900
17:791533:GGC:Gacceptor_gain0.9900
17:791533:GGCTG:Gacceptor_gain0.9900
17:782785:G:GGdonor_gain0.9800
17:783326:GG:Gdonor_gain0.9800
17:783327:GG:Gdonor_gain0.9800
17:782609:G:GTdonor_gain0.9700
17:782662:A:Gdonor_gain0.9700
17:783076:T:Gacceptor_gain0.9700
17:783255:GTC:Gdonor_gain0.9700
17:787963:A:AGacceptor_gain0.9700

AlphaMissense

2739 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
17:791992:A:CS396R0.996
17:791994:C:AS396R0.996
17:791994:C:GS396R0.996
17:791548:T:AW248R0.994
17:791548:T:CW248R0.994
17:783327:G:AG187R0.993
17:783327:G:CG187R0.993
17:787965:G:AG187E0.993
17:788075:G:TG224W0.993
17:783169:C:AA134D0.992
17:783147:G:CG127R0.991
17:783168:G:CA134P0.991
17:783327:G:TG187W0.991
17:788045:T:CC214R0.991
17:788073:T:CL223P0.991
17:791842:T:AW346R0.991
17:791842:T:CW346R0.991
17:792004:T:CF400L0.991
17:792006:C:AF400L0.991
17:792006:C:GF400L0.991
17:783118:G:CR117P0.990
17:783207:A:CS147R0.990
17:783209:C:AS147R0.990
17:783209:C:GS147R0.990
17:791617:T:AW271R0.990
17:791617:T:CW271R0.990
17:791588:T:CF261S0.989
17:788075:G:AG224R0.988
17:788075:G:CG224R0.988
17:791976:C:AN390K0.988

dbSNP variants (sampled 300 via entrez): RS1000189619 (17:789463 G>T), RS1000192306 (17:786700 C>T), RS1000224066 (17:787468 G>T), RS1000291531 (17:792436 A>C,G), RS1000387183 (17:782045 T>G), RS1000635563 (17:780861 A>C), RS1000719775 (17:781078 G>T), RS1000855903 (17:786924 C>G), RS1000933558 (17:787840 C>T), RS1000936512 (17:781164 A>C,T), RS1000969347 (17:786381 C>T), RS1001047437 (17:792430 C>T), RS1001080305 (17:792129 G>A), RS1001467371 (17:785838 T>A), RS1001606920 (17:785430 T>C)

Disease associations

OMIM: gene MIM:612600 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

StudyTraitp-value
GCST001942_3Prostate cancer5.000000e-15

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Benzo(a)pyreneincreases expression, increases methylation4
sodium arseniteincreases abundance, increases expression, decreases expression, affects cotreatment2
Air Pollutantsaffects expression, increases abundance, decreases expression2
aristolochic acid Iincreases expression1
urushioldecreases expression1
trichostatin Aaffects expression, decreases reaction1
tobacco tarincreases expression1
manganese chlorideaffects cotreatment, increases abundance, increases expression1
benzo(e)pyrenedecreases methylation1
aflatoxin B2decreases methylation1
di-n-butylphosphoric acidaffects expression1
cylindrospermopsinincreases expression1
monomethylarsonous aciddecreases expression1
abrinedecreases expression, increases expression1
bisphenol Sincreases expression1
Temozolomideincreases expression1
Arsenicincreases abundance, increases expression, affects cotreatment1
Atrazinedecreases expression1
Carbamazepineaffects expression1
Enzyme Inhibitorsdecreases activity, increases O-linked glycosylation1
Manganeseincreases expression, affects cotreatment, increases abundance1
Methapyrilenedecreases methylation1
Nickelaffects expression, decreases reaction1
Ozoneaffects expression, increases abundance1
Ribonucleotidesaffects binding1
Smokedecreases expression1
Tobacco Smoke Pollutionincreases expression1
Vitamin Eincreases expression1
Cyclosporinedecreases expression1
Aflatoxin B1increases 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.