TRMT61B

gene
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Also known as FLJ20628

Summary

TRMT61B (tRNA methyltransferase 61B, HGNC:26070) is a protein-coding gene on chromosome 2p23.2, encoding tRNA (adenine(58)-N(1))-methyltransferase, mitochondrial (Q9BVS5). Methyltransferase that catalyzes the formation of N(1)-methyladenine at position 58 (m1A58) in various tRNAs in mitochondrion, including tRNA(Leu) (deciphering codons UUA or UUG), tRNA(Lys) and tRNA(Ser) (deciphering codons UCA, UCU, UCG or UCC).

Enables mRNA (adenine-N1-)-methyltransferase activity; rRNA (adenine) methyltransferase activity; and tRNA (adenine(58)-N1)-methyltransferase activity. Involved in mRNA processing and mitochondrial tRNA processing. Located in mitochondrial matrix.

Source: NCBI Gene 55006 — RefSeq curated summary.

At a glance

  • GWAS associations: 2
  • Clinical variants (ClinVar): 97 total
  • MANE Select transcript: NM_017910

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:26070
Approved symbolTRMT61B
NametRNA methyltransferase 61B
Location2p23.2
Locus typegene with protein product
StatusApproved
AliasesFLJ20628
Ensembl geneENSG00000171103
Ensembl biotypeprotein_coding
OMIM619404
Entrez55006

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 9 protein_coding, 1 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000306108, ENST00000419999, ENST00000439947, ENST00000484060, ENST00000490390, ENST00000873366, ENST00000873367, ENST00000873368, ENST00000873369, ENST00000922653, ENST00000922654, ENST00000949006

RefSeq mRNA: 1 — MANE Select: NM_017910 NM_017910

CCDS: CCDS1768

Canonical transcript exons

ENST00000306108 — 7 exons

ExonStartEnd
ENSE000011550292885107228851298
ENSE000011550472886501728865119
ENSE000016605322884982128850242
ENSE000017516912886957928870309
ENSE000035682062885032828850405
ENSE000035760382885240828852499
ENSE000036169802886111828861308

Expression profiles

Bgee: expression breadth ubiquitous, 278 present calls, max score 91.59.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 15.1548 / max 99.6345, expressed in 1789 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
2757215.15481789

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
secondary oocyteCL:000065591.59gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099189.77gold quality
oocyteCL:000002389.15gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047388.25gold quality
heart right ventricleUBERON:000208088.17gold quality
cerebellar hemisphereUBERON:000224586.28gold quality
cerebellar cortexUBERON:000212986.27gold quality
heart left ventricleUBERON:000208486.06gold quality
cardiac ventricleUBERON:000208285.97gold quality
cortical plateUBERON:000534385.80gold quality
ventricular zoneUBERON:000305385.73gold quality
jejunal mucosaUBERON:000039985.70gold quality
left adrenal gland cortexUBERON:003582585.59gold quality
left adrenal glandUBERON:000123485.50gold quality
cerebellumUBERON:000203785.44gold quality
right adrenal glandUBERON:000123385.32gold quality
ganglionic eminenceUBERON:000402385.30gold quality
right adrenal gland cortexUBERON:003582785.17gold quality
duodenumUBERON:000211485.11gold quality
hindlimb stylopod muscleUBERON:000425285.11gold quality
nephron tubuleUBERON:000123185.07gold quality
adrenal cortexUBERON:000123584.97gold quality
right hemisphere of cerebellumUBERON:001489084.97gold quality
adrenal glandUBERON:000236984.87gold quality
mammary ductUBERON:000176584.85gold quality
gastrocnemiusUBERON:000138884.77gold quality
renal glomerulusUBERON:000007484.72gold quality
muscle of legUBERON:000138384.59gold quality
biceps brachiiUBERON:000150784.59gold quality
metanephric glomerulusUBERON:000473684.43gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes3.50

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

44 targeting TRMT61B, 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-3924100.0072.092394
HSA-MIR-223-3P99.9970.141140
HSA-MIR-318599.9968.121959
HSA-MIR-3688-3P99.9772.022834
HSA-MIR-651-3P99.9473.485177
HSA-MIR-806399.9169.763146
HSA-MIR-130599.9171.433443
HSA-MIR-129799.9173.413162
HSA-MIR-367199.9073.043897
HSA-MIR-30A-3P99.8769.742928
HSA-MIR-30D-3P99.8769.922917
HSA-MIR-30E-3P99.8769.682942
HSA-MIR-450399.8571.451869
HSA-MIR-607999.8468.541170
HSA-MIR-469899.8471.414303
HSA-MIR-199A-3P99.7570.48929
HSA-MIR-199B-3P99.7570.48929
HSA-MIR-3129-5P99.7570.46914
HSA-MIR-128399.6972.423009
HSA-MIR-570099.6469.882280
HSA-MIR-3136-3P99.5766.59781
HSA-MIR-7155-3P99.5766.48794
HSA-MIR-4762-5P99.5768.541424
HSA-MIR-451999.4866.10859
HSA-MIR-469699.4867.481040
HSA-MIR-140-5P99.4467.20792
HSA-MIR-19A-5P99.3666.931675
HSA-MIR-19B-1-5P99.3667.071669
HSA-MIR-19B-2-5P99.3667.071669
HSA-MIR-6828-5P99.3169.211433

Literature-anchored findings (GeneRIF, showing 3)

  • Unlike the cytoplasmic tRNA m(1)A58 methyltransferase that consists of an alpha2beta2 heterotetramer formed by Trmt61A and Trmt6, Trmt61B formed a homo-oligomer (presumably a homotetramer) that resembled the bacterial homotetrameric m(1)A58 methyltransferase. (PMID:23097428)
  • 16S rRNA RNA-DNA differences result from a 1-methyladenosine (m1A) modification introduced by TRMT61B. (PMID:27631568)
  • TRMT61B rs4563180 G>C variant reduces hepatoblastoma risk: a case-control study of seven medical centers. (PMID:37531210)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriotrmt61bENSDARG00000097465
drosophila_melanogasterTrmt61FBGN0039407
caenorhabditis_elegansW02A11.1WBGENE00012192

Paralogs (1): TRMT61A (ENSG00000166166)

Protein

Protein identifiers

tRNA (adenine(58)-N(1))-methyltransferase, mitochondrialQ9BVS5 (reviewed: Q9BVS5)

Alternative names: mRNA methyladenosine-N(1)-methyltransferase

All UniProt accessions (3): Q9BVS5, F8WDR2, H7C2E8

UniProt curated annotations — full annotation on UniProt →

Function. Methyltransferase that catalyzes the formation of N(1)-methyladenine at position 58 (m1A58) in various tRNAs in mitochondrion, including tRNA(Leu) (deciphering codons UUA or UUG), tRNA(Lys) and tRNA(Ser) (deciphering codons UCA, UCU, UCG or UCC). Catalyzes the formation of 1-methyladenosine at position 947 of mitochondrial 16S ribosomal RNA and this modification is most likely important for mitoribosomal structure and function. In addition to tRNA N(1)-methyltransferase activity, also acts as a mRNA N(1)-methyltransferase by mediating methylation of adenosine residues at the N(1) position of MT-ND5 mRNA, leading to interfere with mitochondrial translation.

Subunit / interactions. Homooligomer; in contrast to TRMT61A, does not form a heterotetramer.

Subcellular location. Mitochondrion matrix.

Similarity. Belongs to the class I-like SAM-binding methyltransferase superfamily. TRM61 family.

RefSeq proteins (1): NP_060380* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR014816tRNA_MeTrfase_Gcd14Family
IPR029063SAM-dependent_MTases_sfHomologous_superfamily
IPR049470TRM61_CDomain
IPR054151TR61B_FKBP-likeDomain

Pfam: PF08704, PF21985

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

Catalyzed reactions (Rhea), 2 shown:

  • adenosine(58) in tRNA + S-adenosyl-L-methionine = N(1)-methyladenosine(58) in tRNA + S-adenosyl-L-homocysteine + H(+) (RHEA:43152)
  • an adenosine in mRNA + S-adenosyl-L-methionine = an N(1)-methyladenosine in mRNA + S-adenosyl-L-homocysteine + H(+) (RHEA:55392)

UniProt features (45 total): strand 14, region of interest 9, helix 8, binding site 5, compositionally biased region 2, sequence conflict 2, turn 2, transit peptide 1, chain 1, mutagenesis site 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
2B25X-RAY DIFFRACTION2.5

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9BVS5-F172.300.54

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 (5): 259; 278–279; 317; 335; 463

Mutagenesis-validated functional residues (1):

PositionPhenotype
335loss of ability to catalyze the formation of 1-methyladenosine at position 947 of mitochondrial 16s ribosomal rna.

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

IDPathway
R-HSA-6787450tRNA modification in the mitochondrion
R-HSA-9937008Mitochondrial mRNA modification

MSigDB gene sets: 118 (showing top): GOBP_RIBOSOME_BIOGENESIS, GOBP_TRNA_METABOLIC_PROCESS, GOBP_RNA_METHYLATION, GOBP_RNA_MODIFICATION, GOBP_MITOCHONDRIAL_RNA_PROCESSING, E4F1_Q6, GOBP_TRNA_METHYLATION, GOBP_MITOCHONDRIAL_RNA_METABOLIC_PROCESS, LASTOWSKA_COAMPLIFIED_WITH_MYCN, ZHOU_INFLAMMATORY_RESPONSE_LIVE_DN, DODD_NASOPHARYNGEAL_CARCINOMA_UP, TIEN_INTESTINE_PROBIOTICS_24HR_UP, ACEVEDO_LIVER_CANCER_UP, GOBP_RRNA_MODIFICATION, GOBP_METHYLATION

GO Biological Process (6): mRNA processing (GO:0006397), tRNA methylation (GO:0030488), mitochondrial tRNA processing (GO:0090646), tRNA processing (GO:0008033), rRNA methylation (GO:0031167), methylation (GO:0032259)

GO Molecular Function (7): rRNA (adenine) methyltransferase activity (GO:0016433), mRNA (adenine-N1-)-methyltransferase activity (GO:0061953), tRNA (adenine(58)-N1)-methyltransferase activity (GO:0160107), protein binding (GO:0005515), methyltransferase activity (GO:0008168), tRNA (adenine) methyltransferase activity (GO:0016426), transferase activity (GO:0016740)

GO Cellular Component (3): mitochondrion (GO:0005739), mitochondrial matrix (GO:0005759), tRNA (m1A) methyltransferase complex (GO:0031515)

Reactome top-level categories

Rollup of top-2 pathways:

CategoryPathways
tRNA processing1
Metabolism of RNA1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
RNA processing2
RNA methylation2
mRNA metabolic process1
tRNA modification1
mitochondrial RNA metabolic process1
mitochondrial RNA processing1
tRNA processing1
tRNA metabolic process1
rRNA modification1
metabolic process1
rRNA methyltransferase activity1
mRNA methyltransferase activity1
tRNA (adenine) methyltransferase activity1
binding1
transferase activity, transferring one-carbon groups1
tRNA methyltransferase activity1
S-adenosylmethionine-dependent methyltransferase activity1
catalytic activity1
cytoplasm1
intracellular membrane-bounded organelle1
mitochondrion1
intracellular organelle lumen1
tRNA methyltransferase complex1

Protein interactions and networks

STRING

1744 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
TRMT61BTRMT6Q9UJA5918
TRMT61BTRMT10CQ7L0Y3917
TRMT61BTRMT61AQ96FX7893
TRMT61BALKBH1Q13686711
TRMT61BMRM2Q9UI43668
TRMT61BALKBH3Q96Q83667
TRMT61BNSUN4Q96CB9647
TRMT61BMRM3Q9HC36626
TRMT61BRPUSD4Q96CM3624
TRMT61BTRMT2BQ96GJ1621
TRMT61BRRP8O43159596
TRMT61BMETTL1Q9UBP6572
TRMT61BTRUB2O95900568
TRMT61BPUS1Q9Y606568
TRMT61BTRMT5Q32P41567

IntAct

73 interactions, top by confidence:

ABTypeScore
DFFBDFFApsi-mi:“MI:0914”(association)0.940
TRMT61BPPTC7psi-mi:“MI:0914”(association)0.710
TRMT61BFAM9Bpsi-mi:“MI:0915”(physical association)0.670
FAM9BTRMT61Bpsi-mi:“MI:0915”(physical association)0.670
RHODPLXNB2psi-mi:“MI:0914”(association)0.640
IRF7TRMT61Bpsi-mi:“MI:0915”(physical association)0.620
TRMT61BMTIF2psi-mi:“MI:0914”(association)0.610
GRNTRMT61Bpsi-mi:“MI:0915”(physical association)0.560
TRMT61BWFS1psi-mi:“MI:0915”(physical association)0.560
HIKESHICLEC3Apsi-mi:“MI:0914”(association)0.530
POLR1CPOLR3Apsi-mi:“MI:0914”(association)0.530
VTNHAT1psi-mi:“MI:0914”(association)0.530
MRM3NDUFS6psi-mi:“MI:0914”(association)0.530
PPTC7UBBpsi-mi:“MI:0914”(association)0.530
KCTD17CBX4psi-mi:“MI:0914”(association)0.530
NOTCH2ZNF316psi-mi:“MI:0914”(association)0.530
NXT1GLE1psi-mi:“MI:0914”(association)0.530
PNMA2CCDC85Cpsi-mi:“MI:0914”(association)0.530
TRIM10WIZpsi-mi:“MI:0914”(association)0.530
IRF7AIPpsi-mi:“MI:0914”(association)0.500

BioGRID (342): FAM9B (Two-hybrid), TRMT61B (Affinity Capture-MS), TRMT61B (Affinity Capture-MS), TRMT61B (Affinity Capture-MS), TRMT61B (Affinity Capture-MS), TRMT61B (Affinity Capture-MS), TRMT61B (Affinity Capture-MS), TRMT61B (Affinity Capture-MS), TRMT61B (Affinity Capture-MS), TRMT61B (Affinity Capture-MS), TRMT61B (Affinity Capture-MS), TRMT61B (Affinity Capture-MS), TRMT61B (Affinity Capture-MS), TRMT61B (Affinity Capture-MS), CARS2 (Affinity Capture-MS)

ESM2 similar proteins: A4D126, A4II32, A6NDL7, A6QP81, B0K012, E1B8U2, E1BCH6, O55055, O95568, P50747, Q149N8, Q28IN4, Q2KIJ2, Q2T9W2, Q3U2J5, Q498D5, Q4AC99, Q4KM84, Q58DC7, Q5RE14, Q5VZV1, Q6DJF8, Q6GQ33, Q6GR37, Q6ZMV9, Q7SY78, Q7TPQ3, Q80WC9, Q8BLU2, Q8BSE0, Q8C436, Q8CDZ2, Q8K2I9, Q8NE18, Q8NFZ0, Q8WXB1, Q95LL7, Q96EN8, Q96LZ7, Q9BTF0

Diamond homologs: A6H791, O14307, P0CS08, P0CS09, P46959, P9WFZ0, P9WFZ1, Q2U3W4, Q2YY85, Q4WUT7, Q57598, Q5A416, Q5SKN4, Q6AY46, Q6BX32, Q6C0P9, Q6CN53, Q6FL77, Q755M8, Q80XC2, Q86JJ0, Q8GBB2, Q96FX7, Q9BVS5, Q9V1J7, A1AI22, A1SRS4, A4WFY5, A6TGL3, A6UWM1, A7MQL7, A7ZU40, A8A6U0, A8AAV7, A8ACY2, A9MIY3, A9MY97, B1IW72, B1LM21, B1XAJ7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance84
Likely benign4
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1484 predictions. Top by Δscore:

VariantEffectΔscore
2:28850401:TTCTT:Tacceptor_gain1.0000
2:28850403:CTT:Cacceptor_gain1.0000
2:28850406:C:CCacceptor_gain1.0000
2:28850409:T:TCacceptor_gain1.0000
2:28852406:A:ACdonor_gain1.0000
2:28852407:C:CCdonor_gain1.0000
2:28861116:A:ACdonor_gain1.0000
2:28861116:ACTG:Adonor_gain1.0000
2:28861117:C:CCdonor_gain1.0000
2:28861117:CTG:Cdonor_gain1.0000
2:28861117:CTGC:Cdonor_gain1.0000
2:28861310:T:Cacceptor_gain1.0000
2:28849849:GTA:Gacceptor_gain0.9900
2:28850324:TCA:Tdonor_loss0.9900
2:28850325:CACCT:Cdonor_loss0.9900
2:28850326:A:ATdonor_loss0.9900
2:28850404:TT:Tacceptor_gain0.9900
2:28850406:C:Tacceptor_loss0.9900
2:28850407:T:Aacceptor_loss0.9900
2:28850409:T:Cacceptor_gain0.9900
2:28852407:CTTTA:Cdonor_gain0.9900
2:28861117:CT:Cdonor_gain0.9900
2:28861306:CAA:Cacceptor_gain0.9900
2:28861306:CAACT:Cacceptor_gain0.9900
2:28861309:C:CCacceptor_gain0.9900
2:28861314:G:GCacceptor_gain0.9900
2:28850243:C:CCacceptor_gain0.9800
2:28850411:G:Cacceptor_gain0.9800
2:28850411:G:GCacceptor_gain0.9800
2:28861109:AAAAC:Adonor_loss0.9800

AlphaMissense

3094 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
2:28861283:A:CS276R0.983
2:28861283:A:TS276R0.983
2:28861285:T:GS276R0.983
2:28861195:A:GW306R0.981
2:28861195:A:TW306R0.981
2:28865036:G:CS261R0.980
2:28865036:G:TS261R0.980
2:28865038:T:GS261R0.980
2:28865070:A:TV250D0.974
2:28850238:A:CF465L0.972
2:28850238:A:TF465L0.972
2:28850240:A:GF465L0.972
2:28861175:A:CF312L0.954
2:28861175:A:TF312L0.954
2:28861177:A:GF312L0.954
2:28851207:A:GW393R0.948
2:28851207:A:TW393R0.948
2:28861193:C:AW306C0.945
2:28861193:C:GW306C0.945
2:28852427:A:GC356R0.944
2:28861120:C:GA331P0.944
2:28861176:A:GF312S0.944
2:28861308:A:TV268D0.943
2:28865025:G:AS265F0.939
2:28861290:A:TV274D0.938
2:28861231:A:GW294R0.937
2:28861231:A:TW294R0.937
2:28865046:C:TG258D0.927
2:28861251:G:TA287D0.925
2:28851278:A:GL369P0.924

dbSNP variants (sampled 300 via entrez): RS1000176198 (2:28853427 C>T), RS1000176860 (2:28857453 T>C,G), RS1000199297 (2:28862415 C>T), RS1000263038 (2:28865939 C>T), RS1000507133 (2:28853097 A>G), RS1000573364 (2:28870446 T>C), RS1000700670 (2:28870356 G>A,T), RS1000763048 (2:28851812 G>A,C,T), RS1000839018 (2:28864606 G>A), RS1000962675 (2:28857998 A>G), RS1001312311 (2:28864872 G>T), RS1001730242 (2:28869365 G>C), RS1001896877 (2:28871431 T>C), RS1001915421 (2:28863337 G>A), RS1001979806 (2:28858012 G>C)

Disease associations

OMIM: gene MIM:619404 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

StudyTraitp-value
GCST005580_106Intraocular pressure5.000000e-08
GCST007656_7Chronic obstructive pulmonary disease or resting heart rate (pleiotropy)9.000000e-12

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0004695intraocular pressure measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

26 total (human), top 26 by PubMed support.

ChemicalActions (top 5)PubMed papers
Acetaminophendecreases expression, increases expression2
Benzo(a)pyreneaffects methylation, decreases expression2
aristolochic acid Idecreases expression1
GSK-J4decreases expression1
dicrotophosdecreases expression1
bisphenol Adecreases expression1
beta-lapachoneincreases expression1
sodium arsenitedecreases expression1
manganese chlorideincreases abundance, increases expression1
Resveratrolaffects cotreatment, increases expression1
Sunitinibdecreases expression1
Air Pollutantsdecreases expression, increases abundance1
Manganeseincreases expression, increases abundance1
Phthalic Acidsincreases methylation1
Plant Extractsaffects cotreatment, increases expression1
Quercetindecreases expression1
Ribonucleotidesaffects binding1
Seleniumdecreases expression1
Smokedecreases expression1
Urethanedecreases expression1
Valproic Acidaffects expression1
Cyclosporinedecreases expression1
Cadmium Chloridedecreases expression1
Copper Sulfatedecreases expression1
Lactic Aciddecreases expression1
Particulate Matterdecreases expression, increases abundance1

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.