TRMT6

gene
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Also known as GCD10MGC5029Gcd10pCGI-09

Summary

TRMT6 (tRNA methyltransferase 6 non-catalytic subunit, HGNC:20900) is a protein-coding gene on chromosome 20p12.3, encoding tRNA (adenine(58)-N(1))-methyltransferase non-catalytic subunit TRM6 (Q9UJA5). Substrate-binding subunit of tRNA (adenine-N(1)-)-methyltransferase, which catalyzes the formation of N(1)-methyladenine at position 58 (m1A58) in initiator methionyl-tRNA. It is a selective cancer dependency (DepMap: 35.5% of cell lines).

This gene encodes a member of the tRNA methyltransferase 6 protein family. A similar protein in yeast is part of a two component methyltransferase, which is involved in the posttranslational modification that produces the modified nucleoside 1-methyladenosine in tRNAs. Modified 1-methyladenosine influences initiator methionine stability and may be involved in the replication of human immunodeficiency virus type 1. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 51605 — RefSeq curated summary.

At a glance

  • GWAS associations: 3
  • Clinical variants (ClinVar): 70 total
  • Cancer dependency (DepMap): dependent in 35.5% of screened cell lines
  • MANE Select transcript: NM_015939

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:20900
Approved symbolTRMT6
NametRNA methyltransferase 6 non-catalytic subunit
Location20p12.3
Locus typegene with protein product
StatusApproved
AliasesGCD10, MGC5029, Gcd10p, CGI-09
Ensembl geneENSG00000089195
Ensembl biotypeprotein_coding
OMIM620886
Entrez51605

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 6 protein_coding, 3 protein_coding_CDS_not_defined

ENST00000203001, ENST00000453074, ENST00000466974, ENST00000473131, ENST00000493972, ENST00000931286, ENST00000931287, ENST00000931288, ENST00000931289

RefSeq mRNA: 2 — MANE Select: NM_015939 NM_001281467, NM_015939

CCDS: CCDS13093, CCDS63225

Canonical transcript exons

ENST00000203001 — 11 exons

ExonStartEnd
ENSE0000171445159502785950533
ENSE0000347876159439485944031
ENSE0000350809259412435941345
ENSE0000352605059464065946533
ENSE0000353397759410535941139
ENSE0000357196659424285942786
ENSE0000359663459435595943683
ENSE0000360688959448055944914
ENSE0000363114559441625944253
ENSE0000363950159419515942036
ENSE0000384762259372285938726

Expression profiles

Bgee: expression breadth ubiquitous, 257 present calls, max score 96.44.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 13.9188 / max 267.7466, expressed in 1770 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
18633411.27481759
1863332.64391050

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
secondary oocyteCL:000065596.44gold quality
oocyteCL:000002396.22gold quality
upper arm skinUBERON:000426391.35gold quality
nippleUBERON:000203090.14gold quality
kidney epitheliumUBERON:000481989.69gold quality
seminal vesicleUBERON:000099889.31gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047389.08gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099189.07gold quality
cerebellar vermisUBERON:000472088.73gold quality
parotid glandUBERON:000183187.48gold quality
nasal cavity epitheliumUBERON:000538487.37gold quality
ponsUBERON:000098887.24gold quality
bone marrowUBERON:000237187.21gold quality
islet of LangerhansUBERON:000000686.58gold quality
monocyteCL:000057686.51gold quality
gastrocnemiusUBERON:000138886.45gold quality
pericardiumUBERON:000240786.41gold quality
Brodmann (1909) area 23UBERON:001355486.38gold quality
leukocyteCL:000073886.29gold quality
pylorusUBERON:000116686.20gold quality
deltoidUBERON:000147686.18gold quality
tendon of biceps brachiiUBERON:000818886.16gold quality
mammalian vulvaUBERON:000099785.97gold quality
substantia nigra pars compactaUBERON:000196585.85gold quality
gingival epitheliumUBERON:000194985.67gold quality
renal medullaUBERON:000036285.59gold quality
muscle of legUBERON:000138385.49gold quality
synovial jointUBERON:000221785.49gold quality
trabecular bone tissueUBERON:000248385.46gold quality
gingivaUBERON:000182885.39gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 2.

ExperimentMarker?Max mean expression
E-ANND-3yes18.46
E-MTAB-9467yes11.25
E-GEOD-110499no2044.06

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

46 targeting TRMT6, 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-3613-3P100.0076.367965
HSA-MIR-3667-3P99.9967.171636
HSA-MIR-146A-5P99.9668.93988
HSA-MIR-146B-5P99.9669.13977
HSA-MIR-391099.9571.132227
HSA-MIR-7153-5P99.9468.891006
HSA-MIR-153-5P99.8973.866317
HSA-MIR-182-5P99.8774.032589
HSA-MIR-6875-3P99.8270.262983
HSA-MIR-4677-5P99.7070.091940
HSA-MIR-545-5P99.6670.182308
HSA-MIR-7157-5P99.6669.331829
HSA-MIR-10394-5P99.6566.831852
HSA-MIR-120599.6566.761826
HSA-MIR-570099.6469.882280
HSA-MIR-561-3P99.6470.903647
HSA-MIR-5197-5P99.6469.081494
HSA-MIR-651-5P99.6468.491104
HSA-MIR-431099.5968.842527
HSA-MIR-513C-5P99.5068.421730
HSA-MIR-514B-5P99.5068.191766
HSA-MIR-142-5P99.4870.922416
HSA-MIR-5590-3P99.4870.912429
HSA-MIR-150-3P99.4370.51920
HSA-MIR-425199.4069.193363
HSA-MIR-127699.3668.181642
HSA-MIR-6507-5P99.3670.462524
HSA-MIR-2116-5P99.3269.341273
HSA-MIR-432499.0470.141569
HSA-MIR-4709-3P98.8868.041594

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 35.5% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 4)

  • TRMT6 was upregulated in HCC tissues, and higher TRMT6 expression levels was correlated with reduced OS and RFS in patients with primary HCC. (PMID:31128068)
  • N(1)-methyladenosine methylation in tRNA drives liver tumourigenesis by regulating cholesterol metabolism. (PMID:34728628)
  • TRMT6 gene rs236110 C > A polymorphism increases the risk of Wilms tumor. (PMID:37473973)
  • Identification of hepatoblastoma susceptibility loci in the TRMT6 gene from a seven-center case-control study. (PMID:37850543)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriotrmt6ENSDARG00000042344
mus_musculusTrmt6ENSMUSG00000037376
rattus_norvegicusTrmt6ENSRNOG00000021270
drosophila_melanogasterTrmt6FBGN0031832
caenorhabditis_eleganstrmt-6WBGENE00014120

Protein

Protein identifiers

tRNA (adenine(58)-N(1))-methyltransferase non-catalytic subunit TRM6Q9UJA5 (reviewed: Q9UJA5)

Alternative names: mRNA methyladenosine-N(1)-methyltransferase non-catalytic subunit TRM6, tRNA(m1A58)-methyltransferase subunit TRM6

All UniProt accessions (1): Q9UJA5

UniProt curated annotations — full annotation on UniProt →

Function. Substrate-binding subunit of tRNA (adenine-N(1)-)-methyltransferase, which catalyzes the formation of N(1)-methyladenine at position 58 (m1A58) in initiator methionyl-tRNA. Together with the TRMT61A catalytic subunit, part of a mRNA N(1)-methyltransferase complex that mediates methylation of adenosine residues at the N(1) position of a small subset of mRNAs: N(1) methylation takes place in tRNA T-loop-like structures of mRNAs and is only present at low stoichiometries.

Subunit / interactions. Heterotetramer; composed of two copies of TRMT6 and two copies of TRMT61A.

Subcellular location. Nucleus.

Tissue specificity. Expressed in brain, liver, testis and ovary.

Similarity. Belongs to the TRM6/GCD10 family.

Isoforms (4)

UniProt IDNamesCanonical?
Q9UJA5-11yes
Q9UJA5-22
Q9UJA5-33
Q9UJA5-44

RefSeq proteins (2): NP_001268396, NP_057023* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR017423TRM6Family

Pfam: PF04189

Enzyme classification (BRENDA):

  • EC 2.1.1.220 — tRNA (adenine58-N1)-methyltransferase (BRENDA: 8 organisms, 17 substrates, 2 inhibitors, 5 Km, 0 kcat entries)

Substrate kinetics (BRENDA)

3 substrates with measured Km, best-characterized 3. Km ranges are aggregated across organisms/conditions.

SubstrateKm (mM)Measurements
ADENINE58 IN INITIATOR TRNAMET1
ADENINE58 IN TRNAPHE0.00011
S-ADENOSYL-L-METHIONINE0.0051

UniProt features (59 total): strand 17, helix 17, binding site 7, region of interest 4, splice variant 4, modified residue 3, sequence variant 3, compositionally biased region 3, chain 1

Structure

Experimental structures (PDB)

3 structures.

PDBMethodResolution (Å)
5CCBX-RAY DIFFRACTION2
5CCXX-RAY DIFFRACTION2.1
5CD1X-RAY DIFFRACTION3.6

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9UJA5-F180.020.61

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 (7): 175–182; 349; 377; 415–423; 434–441; 94–104; 145–154

Post-translational modifications (3): 107, 298, 305

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-6782315tRNA modification in the nucleus and cytosol

MSigDB gene sets: 136 (showing top): E2F_Q4, RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP, E2F4DP1_01, GOBP_TRNA_METABOLIC_PROCESS, CHANDRAN_METASTASIS_DN, GOBP_RNA_METHYLATION, MONNIER_POSTRADIATION_TUMOR_ESCAPE_UP, WEI_MYCN_TARGETS_WITH_E_BOX, E2F1DP1_01, E2F_Q3, E2F1DP2_01, GOBP_RNA_MODIFICATION, GOBP_TRNA_METHYLATION, GARCIA_TARGETS_OF_FLI1_AND_DAX1_DN, CHARAFE_BREAST_CANCER_LUMINAL_VS_BASAL_DN

GO Biological Process (3): mRNA processing (GO:0006397), tRNA methylation (GO:0030488), tRNA processing (GO:0008033)

GO Molecular Function (2): RNA binding (GO:0003723), protein binding (GO:0005515)

GO Cellular Component (3): nucleus (GO:0005634), nucleoplasm (GO:0005654), tRNA (m1A) methyltransferase complex (GO:0031515)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
tRNA processing1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
RNA processing2
mRNA metabolic process1
RNA methylation1
tRNA modification1
tRNA metabolic process1
nucleic acid binding1
binding1
intracellular membrane-bounded organelle1
nuclear lumen1
cellular anatomical structure1
tRNA methyltransferase complex1

Protein interactions and networks

STRING

1988 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
TRMT6TRMT61AQ96FX7999
TRMT6TRMT61BQ9BVS5918
TRMT6TRMT10CQ7L0Y3850
TRMT6ALKBH1Q13686776
TRMT6METTL1Q9UBP6744
TRMT6WDR4P57081718
TRMT6TRMT5Q32P41718
TRMT6TRMT112Q9UI30718
TRMT6TRMT11Q7Z4G4712
TRMT6NSUN2Q08J23711
TRMT6ALKBH3Q96Q83709
TRMT6FTSJ1Q9UET6691
TRMT6TRUB1Q8WWH5676
TRMT6TRMT10AQ8TBZ6661
TRMT6ADAT3Q96EY9645

IntAct

98 interactions, top by confidence:

ABTypeScore
SRP9SRP72psi-mi:“MI:0914”(association)0.730
TRMT61ATRMT6psi-mi:“MI:0915”(physical association)0.670
USE1NBASpsi-mi:“MI:0914”(association)0.640
KLHL22TMEM223psi-mi:“MI:0914”(association)0.640
TRMT6PPIApsi-mi:“MI:0915”(physical association)0.560
TRMT6YWHAGpsi-mi:“MI:0915”(physical association)0.560
TRMT6SETDB1psi-mi:“MI:0915”(physical association)0.560
TRMT6KAT5psi-mi:“MI:0915”(physical association)0.560
LMO3TRMT6psi-mi:“MI:0915”(physical association)0.560
TRMT61AARHGEF11psi-mi:“MI:0914”(association)0.530
PTGES3AIPpsi-mi:“MI:0914”(association)0.530
MAGEB2GTPBP10psi-mi:“MI:0914”(association)0.530
RPL4TEFMpsi-mi:“MI:0914”(association)0.530
TRMT6FOXJ1psi-mi:“MI:0915”(physical association)0.370
TRMT6HHEXpsi-mi:“MI:0915”(physical association)0.370
CKAP5TACC3psi-mi:“MI:0914”(association)0.350
NETO2TIA1psi-mi:“MI:0914”(association)0.350

BioGRID (128): TRMT6 (Affinity Capture-MS), TRMT6 (Affinity Capture-MS), TRMT6 (Affinity Capture-MS), TRMT6 (Affinity Capture-MS), DDX5 (Co-fractionation), DNAJC17 (Co-fractionation), EIF2B1 (Co-fractionation), NHP2L1 (Co-fractionation), PUS1 (Co-fractionation), RDX (Co-fractionation), SNW1 (Co-fractionation), STK24 (Co-fractionation), TLN2 (Co-fractionation), TRMT6 (Co-fractionation), TRMT6 (Co-fractionation)

ESM2 similar proteins: A0A3Q1LSX9, A2APV2, A4IHK8, A8K855, A9JRL3, D3Z8X7, O00418, O08796, O35099, O60308, P55265, P70531, Q13905, Q1LX49, Q28CB1, Q3SXY8, Q3UFM5, Q4V8B2, Q5E9V1, Q5QNQ6, Q5R6Y9, Q5R9G1, Q5RHX6, Q62172, Q62796, Q640N2, Q66JG9, Q6DD21, Q6DFA1, Q6ZPF4, Q7Z699, Q7ZYB4, Q80V31, Q80V94, Q8CI95, Q8IVF7, Q8IWE4, Q8K0Q5, Q8K0V2, Q8K4M9

Diamond homologs: Q2T9V5, Q4WE58, Q54UB1, Q8CE96, Q9UJA5, Q2UJ66

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 97 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
SRP-dependent cotranslational protein targeting to membrane79.5×4e-03
Formation of a pool of free 40S subunits69.1×8e-03
L13a-mediated translational silencing of Ceruloplasmin expression68.2×8e-03
GTP hydrolysis and joining of the 60S ribosomal subunit68.1×8e-03
Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC)67.9×8e-03

GO biological processes:

GO termPartnersFoldFDR
cytoplasmic translation612.2×4e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance53
Likely benign3
Benign2

Top pathogenic / likely-pathogenic (0)

SpliceAI

1569 predictions. Top by Δscore:

VariantEffectΔscore
20:5938726:CCTAA:Cacceptor_loss1.0000
20:5938727:CTA:Cacceptor_loss1.0000
20:5941048:CGTA:Cdonor_loss1.0000
20:5941049:GTACC:Gdonor_loss1.0000
20:5941050:TA:Tdonor_loss1.0000
20:5941051:ACC:Adonor_loss1.0000
20:5941052:CCTGA:Cdonor_loss1.0000
20:5941136:GAGG:Gacceptor_gain1.0000
20:5941140:C:CCacceptor_gain1.0000
20:5941341:TTAAA:Tacceptor_gain1.0000
20:5941346:C:CCacceptor_gain1.0000
20:5941938:T:TAdonor_gain1.0000
20:5941950:CCCAT:Cdonor_gain1.0000
20:5941973:G:Cdonor_gain1.0000
20:5942421:T:TAdonor_gain1.0000
20:5942426:A:ACdonor_gain1.0000
20:5942427:C:CCdonor_gain1.0000
20:5942430:AAT:Adonor_gain1.0000
20:5942443:T:TAdonor_gain1.0000
20:5942455:AGGCC:Adonor_gain1.0000
20:5942489:T:TAdonor_gain1.0000
20:5942498:T:Adonor_gain1.0000
20:5943554:CTTA:Cdonor_loss1.0000
20:5943556:TA:Tdonor_loss1.0000
20:5943557:A:ACdonor_gain1.0000
20:5943557:ACCT:Adonor_gain1.0000
20:5943557:ACCTC:Adonor_gain1.0000
20:5943558:C:CCdonor_gain1.0000
20:5943558:C:CTdonor_loss1.0000
20:5943558:CCT:Cdonor_gain1.0000

AlphaMissense

3276 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
20:5938708:G:CH441D1.000
20:5944183:T:CY146C1.000
20:5944184:A:GY146H1.000
20:5944206:C:AK138N1.000
20:5944206:C:GK138N1.000
20:5944215:G:CF135L1.000
20:5944215:G:TF135L1.000
20:5944217:A:GF135L1.000
20:5944237:A:GL128S1.000
20:5944854:A:GL106P1.000
20:5944859:C:AQ104H1.000
20:5944859:C:GQ104H1.000
20:5944887:C:GR95P1.000
20:5938713:C:GR439P0.999
20:5941062:T:AR431S0.999
20:5941062:T:GR431S0.999
20:5941063:C:AR431I0.999
20:5941063:C:GR431T0.999
20:5944170:C:AK150N0.999
20:5944170:C:GK150N0.999
20:5944172:T:CK150E0.999
20:5944183:T:GY146S0.999
20:5944184:A:CY146D0.999
20:5944185:T:AK145N0.999
20:5944185:T:GK145N0.999
20:5944186:T:AK145I0.999
20:5944187:T:CK145E0.999
20:5944191:T:AQ143H0.999
20:5944191:T:GQ143H0.999
20:5944195:G:TA142D0.999

dbSNP variants (sampled 300 via entrez): RS1000293469 (20:5949977 G>A), RS1000402164 (20:5949304 T>C), RS1000696039 (20:5938532 G>A,C), RS1000922968 (20:5943797 T>C,G), RS1001425755 (20:5940761 G>A,T), RS1002243875 (20:5945106 G>T), RS1002343414 (20:5950566 G>T), RS1002418498 (20:5951055 A>G), RS1002504259 (20:5947732 C>A,G,T), RS1002856021 (20:5948198 G>A,C), RS1002967038 (20:5948037 T>C), RS1003562129 (20:5949248 C>T), RS1003648188 (20:5949127 T>G), RS1003734138 (20:5942548 A>G,T), RS1003855333 (20:5949930 G>A)

Disease associations

OMIM: gene MIM:620886 | 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
GCST000403_1Menarche and menopause (age at onset)1.000000e-21
GCST009158_7Uterine fibroids9.000000e-10
GCST012316_9ghrelin levels7.000000e-07

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0004704age at menopause
EFO:0600001ghrelin measurement

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
sodium arsenitedecreases expression, increases expression2
Resveratrolaffects cotreatment, increases expression2
Air Pollutantsincreases oxidation, decreases expression, affects cotreatment, increases abundance2
Valproic Acidincreases expression, decreases methylation2
methylmercuric chlorideincreases expression1
triphenyl phosphateaffects expression1
alpha-pineneaffects cotreatment, increases oxidation, increases abundance1
bisphenol Adecreases expression1
deoxynivalenolincreases expression1
mono-(2-ethylhexyl)phthalatedecreases expression1
nickel sulfatedecreases expression1
methacrylaldehydeincreases oxidation, increases abundance, affects cotreatment1
ICG 001decreases expression1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic aciddecreases expression1
Sunitinibincreases expression1
Acroleinincreases abundance, affects cotreatment, increases oxidation1
Benzo(a)pyreneincreases mutagenesis1
Coumestrolaffects cotreatment, increases expression1
Dinitrochlorobenzeneaffects binding1
Estradiolincreases expression1
Hydrogen Peroxideaffects expression1
Nickelincreases expression1
Ozoneincreases oxidation, increases abundance, affects cotreatment1
Plant Extractsaffects cotreatment, increases expression1
Ribonucleotidesaffects binding1
Smokedecreases expression1
Tobacco Smoke Pollutionincreases expression1
Urethanedecreases expression1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxideincreases expression1
Cyclosporineincreases expression1

Clinical trials (associated diseases)

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

  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): uterine corpus leiomyoma