TRMT11

Summary

TRMT11 (tRNA methyltransferase 11, HGNC:21080) is a protein-coding gene on chromosome 6q22.32, encoding tRNA (guanine(10)-N(2))-methyltransferase TRMT11 (Q7Z4G4). Catalytic subunit of the TRMT11-TRM112 methyltransferase complex, that specifically mediates the S-adenosyl-L-methionine-dependent N(2)-methylation of guanosine nucleotide at position 10 (m2G10) in tRNAs.

Enables tRNA (guanine(10)-N2)-methyltransferase activity. Predicted to be involved in methylation and tRNA processing. Located in mitochondrion. Part of tRNA (m2G10) methyltransferase complex. Is active in cytoplasm.

Source: NCBI Gene 60487 — RefSeq curated summary.

At a glance

• GWAS associations: 10
• Clinical variants (ClinVar): 82 total
• MANE Select transcript: NM_001031712

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:21080
Approved symbol	TRMT11
Name	tRNA methyltransferase 11
Location	6q22.32
Locus type	gene with protein product
Status	Approved
Aliases	MDS024, dJ187J11.2, TRM11, TRMT11-1
Ensembl gene	ENSG00000066651
Ensembl biotype	protein_coding
Entrez	60487

Gene structure

Transcript identifiers

Ensembl transcripts: 18 — 11 protein_coding, 5 nonsense_mediated_decay, 2 protein_coding_CDS_not_defined

ENST00000334379, ENST00000368332, ENST00000444121, ENST00000444229, ENST00000446681, ENST00000461129, ENST00000466316, ENST00000468097, ENST00000473273, ENST00000479748, ENST00000489934, ENST00000648977, ENST00000873977, ENST00000873978, ENST00000873979, ENST00000935693, ENST00000935694, ENST00000935695

RefSeq mRNA: 19 — MANE Select: NM_001031712 NM_001031712, NM_001350580, NM_001350581, NM_001350582, NM_001350583, NM_001350584, NM_001350585, NM_001350586, NM_001350587, NM_001350588, NM_001350589, NM_001350590, NM_001350591, NM_001350592, NM_001350593, NM_001350594, NM_001350595, NM_001350596, NM_001350597

CCDS: CCDS35496

Canonical transcript exons

ENST00000334379 — 13 exons

Exon	Start	End
ENSE00002256311	125986540	125986622
ENSE00003471889	125995967	125996040
ENSE00003481831	126038705	126039276
ENSE00003573249	126011253	126011417
ENSE00003605756	126012970	126013101
ENSE00003615483	125998223	125998315
ENSE00003615773	125999457	125999613
ENSE00003639661	126008392	126008472
ENSE00003647076	125998550	125998684
ENSE00003660047	125993757	125993822
ENSE00003671611	126012771	126012852
ENSE00003703739	126021160	126021280
ENSE00003785587	125998053	125998134

Expression profiles

Bgee: expression breadth ubiquitous, 283 present calls, max score 95.25.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 28.6550 / max 406.6553, expressed in 1802 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter ID	TPM avg	Samples expressed
69695	18.2466	1760
69692	7.3384	1726
69696	1.2202	646
69694	0.9531	585
69693	0.8403	485
69697	0.0564	19

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
secondary oocyte	CL:0000655	95.25	gold quality
calcaneal tendon	UBERON:0003701	93.91	gold quality
oocyte	CL:0000023	92.50	gold quality
mucosa of stomach	UBERON:0001199	92.13	gold quality
right lobe of liver	UBERON:0001114	90.01	gold quality
adenohypophysis	UBERON:0002196	89.99	gold quality
ventricular zone	UBERON:0003053	89.73	gold quality
tendon	UBERON:0000043	89.72	gold quality
pituitary gland	UBERON:0000007	89.53	gold quality
caput epididymis	UBERON:0004358	89.51	gold quality
right hemisphere of cerebellum	UBERON:0014890	89.49	gold quality
cerebellar hemisphere	UBERON:0002245	89.45	gold quality
cerebellar cortex	UBERON:0002129	89.35	gold quality
jejunal mucosa	UBERON:0000399	89.24	gold quality
blood vessel layer	UBERON:0004797	89.08	gold quality
body of uterus	UBERON:0009853	88.91	gold quality
cerebellum	UBERON:0002037	88.64	gold quality
adrenal tissue	UBERON:0018303	88.16	gold quality
cartilage tissue	UBERON:0002418	88.01	gold quality
liver	UBERON:0002107	87.96	gold quality
duodenum	UBERON:0002114	87.91	gold quality
corpus callosum	UBERON:0002336	87.89	gold quality
descending thoracic aorta	UBERON:0002345	87.84	gold quality
left ovary	UBERON:0002119	87.75	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	87.60	gold quality
right ovary	UBERON:0002118	87.39	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	87.36	gold quality
right uterine tube	UBERON:0001302	87.35	gold quality
cauda epididymis	UBERON:0004360	87.30	gold quality
tibia	UBERON:0000979	87.29	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	6.76

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 1)

• SNPs associated with androgen deprivation failure in advanced prostate cancer (PMID:22386179)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	trmt11	ENSDARG00000040033
mus_musculus	Trmt11	ENSMUSG00000019792
rattus_norvegicus	Trmt11	ENSRNOG00000014240
drosophila_melanogaster	CG1074	FBGN0037250
caenorhabditis_elegans	Y71F9AL.1	WBGENE00022107

Protein

Protein identifiers

tRNA (guanine(10)-N(2))-methyltransferase TRMT11 — Q7Z4G4 (reviewed: Q7Z4G4)

Alternative names: tRNA methyltransferase 11 homolog

All UniProt accessions (7): Q7Z4G4, K7EJQ4, K7ENP1, K7EPZ4, Q5JY01, Q5JY02, V9GXZ6

UniProt curated annotations — full annotation on UniProt →

Function. Catalytic subunit of the TRMT11-TRM112 methyltransferase complex, that specifically mediates the S-adenosyl-L-methionine-dependent N(2)-methylation of guanosine nucleotide at position 10 (m2G10) in tRNAs. This is one of the major tRNA (guanine-N(2))-methyltransferases.

Subunit / interactions. Part of the heterodimeric TRMT11-TRM112 methyltransferase complex; this complex forms an active tRNA methyltransferase, where TRMT112 acts as an activator of the catalytic subunit TRMT11.

Subcellular location. Cytoplasm.

Similarity. Belongs to the class I-like SAM-binding methyltransferase superfamily. TRM11 methyltransferase family.

Isoforms (3)

UniProt ID	Names	Canonical?
Q7Z4G4-1	1	yes
Q7Z4G4-2	2
Q7Z4G4-3	3

RefSeq proteins (19): NP_001026882, NP_001337509, NP_001337510, NP_001337511, NP_001337512, NP_001337513, NP_001337514, NP_001337515, NP_001337516, NP_001337517, NP_001337518, NP_001337519, NP_001337520, NP_001337521, NP_001337522, NP_001337523, NP_001337524, NP_001337525, NP_001337526 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000241	RlmKL-like_Mtase	Domain
IPR002052	DNA_methylase_N6_adenine_CS	Conserved_site
IPR016691	TRMT11	Family
IPR029063	SAM-dependent_MTases_sf	Homologous_superfamily
IPR059073	TRMT11_N	Domain

Pfam: PF01170, PF25904

Catalyzed reactions (Rhea), 1 shown:

• guanosine(10) in tRNA + S-adenosyl-L-methionine = N(2)-methylguanosine(10) in tRNA + S-adenosyl-L-homocysteine + H(+) (RHEA:43128)

UniProt features (7 total): splice variant 3, initiator methionine 1, chain 1, modified residue 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q7Z4G4-F1	88.53	0.69

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): 2

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-6782315	tRNA modification in the nucleus and cytosol

MSigDB gene sets: 109 (showing top): GSE45365_CD8A_DC_VS_CD11B_DC_IFNAR_KO_DN, GSE18804_SPLEEN_MACROPHAGE_VS_TUMORAL_MACROPHAGE_DN, WENDT_COHESIN_TARGETS_UP, GOBP_TRNA_METABOLIC_PROCESS, GOBP_RNA_METHYLATION, KEGG_HISTIDINE_METABOLISM, GOBP_RNA_MODIFICATION, DEURIG_T_CELL_PROLYMPHOCYTIC_LEUKEMIA_DN, MILI_PSEUDOPODIA_HAPTOTAXIS_UP, GGAANCGGAANY_UNKNOWN, TGTGTGA_MIR377, ZHANG_BREAST_CANCER_PROGENITORS_UP, GGTGAAG_MIR412, GOBP_METHYLATION, GOBP_TRNA_PROCESSING

GO Biological Process (3): tRNA processing (GO:0008033), methylation (GO:0032259), RNA processing (GO:0006396)

GO Molecular Function (7): tRNA binding (GO:0000049), methyltransferase activity (GO:0008168), tRNA (guanine(10)-N2)-methyltransferase activity (GO:0160102), nucleic acid binding (GO:0003676), RNA binding (GO:0003723), protein binding (GO:0005515), transferase activity (GO:0016740)

GO Cellular Component (3): cytoplasm (GO:0005737), mitochondrion (GO:0005739), tRNA (m2G10) methyltransferase complex (GO:0043528)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
tRNA processing	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	2
RNA processing	1
tRNA metabolic process	1
metabolic process	1
gene expression	1
RNA biosynthetic process	1
primary metabolic process	1
RNA binding	1
transferase activity, transferring one-carbon groups	1
N-methyltransferase activity	1
tRNA (guanine) methyltransferase activity	1
nucleic acid binding	1
catalytic activity	1
intracellular anatomical structure	1
cellular anatomical structure	1
cytoplasm	1
intracellular membrane-bounded organelle	1
tRNA methyltransferase complex	1

Protein interactions and networks

STRING

1522 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TRMT11	TRMT112	Q9UI30	986
TRMT11	TRMT1	Q9NXH9	855
TRMT11	HEMK2	Q9Y5N5	811
TRMT11	BUD23	O43709	794
TRMT11	ALKBH8	Q96BT7	736
TRMT11	TRMT61A	Q96FX7	718
TRMT11	FTSJ1	Q9UET6	717
TRMT11	TRMT6	Q9UJA5	712
TRMT11	TRMT5	Q32P41	693
TRMT11	METTL1	Q9UBP6	667
TRMT11	WDR4	P57081	648
TRMT11	THUMPD2	Q9BTF0	624
TRMT11	NSUN2	Q08J23	616
TRMT11	MACIR	Q96GV9	612
TRMT11	TRMT9B	Q9P272	607

IntAct

29 interactions, top by confidence:

A	B	Type	Score
TRMT112	BUD23	psi-mi:“MI:0914”(association)	0.910
AKR7A3	AKR7A2	psi-mi:“MI:0914”(association)	0.890
HSPD1	NUDT19	psi-mi:“MI:0914”(association)	0.710
TRMT11	TRMT112	psi-mi:“MI:0915”(physical association)	0.650
TRMT11	TRMT112	psi-mi:“MI:0403”(colocalization)	0.650
TRMT11	DCDC2	psi-mi:“MI:0915”(physical association)	0.560
TRMT11	LHX4	psi-mi:“MI:0915”(physical association)	0.560
PLAUR	XRCC3	psi-mi:“MI:0914”(association)	0.530
TRMT11	RPL27A	psi-mi:“MI:0915”(physical association)	0.400
HSCB	RBP5	psi-mi:“MI:0914”(association)	0.350
WDR48	UNC13B	psi-mi:“MI:0914”(association)	0.350
RAMP2	GXYLT2	psi-mi:“MI:0914”(association)	0.350
DNAJA2	DENND11	psi-mi:“MI:0914”(association)	0.350
TRMT11	NARS1	psi-mi:“MI:0914”(association)	0.350
SSX6P	MDM2	psi-mi:“MI:0914”(association)	0.350
FECH	GTPBP10	psi-mi:“MI:0914”(association)	0.350
	VWA8	psi-mi:“MI:2364”(proximity)	0.270
HSPD1	VWA8	psi-mi:“MI:2364”(proximity)	0.270
MGST3	VWA8	psi-mi:“MI:2364”(proximity)	0.270
PDK1	VWA8	psi-mi:“MI:2364”(proximity)	0.270
TRMT61B	VWA8	psi-mi:“MI:2364”(proximity)	0.270
TRMT11	LHX4	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (49): TRMT11 (Affinity Capture-MS), TRMT11 (Affinity Capture-MS), GALC (Affinity Capture-MS), TRMT112 (Affinity Capture-MS), NARS (Affinity Capture-MS), TRMT11 (Affinity Capture-MS), TRMT11 (Affinity Capture-MS), TRMT11 (Proximity Label-MS), TRMT11 (Proximity Label-MS), TRMT11 (Proximity Label-MS), TRMT11 (Proximity Label-MS), TRMT11 (Synthetic Lethality), LHX4 (Two-hybrid), TRMT11 (Proximity Label-MS), TRMT11 (Affinity Capture-MS)

ESM2 similar proteins: A0A1J6KGJ9, A0A314KSQ4, A2RU49, A4IF87, A5PJU6, B4G0F3, B8BKI7, B9SQI7, C6JS30, E0CSI1, E0CTF3, G1SPE9, O08848, O15228, O22190, O23732, O43929, O82333, O88708, P11172, P31531, P37821, P42700, P46416, Q05B63, Q10D00, Q28DB5, Q2R483, Q2YDI2, Q3T067, Q3U1V6, Q4U3P8, Q5R514, Q5R6Z7, Q5R962, Q6GM82, Q6I581, Q6YJI5, Q7TNK6, Q7Z4G4

Diamond homologs: O26820, O94636, P05409, Q05B63, Q12463, Q54QA6, Q58120, Q5R962, Q6NS23, Q6YJI5, Q7TNK6, Q7Z4G4, Q9CWH5, O29011, Q9UY84

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
TRMT11	“form complex”	“TRMT11-TRM112 methyltransferase complex”	binding

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	70
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2721 predictions. Top by Δscore:

Variant	Effect	Δscore
6:125986710:G:GT	donor_gain	1.0000
6:125995965:A:AG	acceptor_gain	1.0000
6:125995966:G:GA	acceptor_gain	1.0000
6:125995966:GTC:G	acceptor_gain	1.0000
6:125996041:G:GG	donor_gain	1.0000
6:125998131:GATG:G	donor_gain	1.0000
6:125998132:ATGG:A	donor_loss	1.0000
6:125998133:TGGT:T	donor_loss	1.0000
6:125998136:T:A	donor_loss	1.0000
6:125998217:TTTTA:T	acceptor_loss	1.0000
6:125998219:TTAG:T	acceptor_loss	1.0000
6:125998220:TA:T	acceptor_loss	1.0000
6:125998221:A:AG	acceptor_gain	1.0000
6:125998221:AGGTT:A	acceptor_loss	1.0000
6:125998222:G:GG	acceptor_gain	1.0000
6:125998311:TAGAT:T	donor_gain	1.0000
6:125998312:AGAT:A	donor_gain	1.0000
6:125998313:GAT:G	donor_gain	1.0000
6:125998313:GATG:G	donor_gain	1.0000
6:125998314:AT:A	donor_gain	1.0000
6:125998315:TG:T	donor_loss	1.0000
6:125998316:G:GG	donor_gain	1.0000
6:125998316:GTA:G	donor_loss	1.0000
6:125998317:T:G	donor_loss	1.0000
6:125998320:G:GG	donor_gain	1.0000
6:125999455:A:AG	acceptor_gain	1.0000
6:125999456:G:GG	acceptor_gain	1.0000
6:125999456:GA:G	acceptor_gain	1.0000
6:126011251:A:AC	acceptor_loss	1.0000
6:126011251:A:AG	acceptor_gain	1.0000

AlphaMissense

3058 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
6:125999526:A:C	S198R	0.999
6:125999528:T:A	S198R	0.999
6:125999528:T:G	S198R	0.999
6:126012786:G:C	R314T	0.999
6:126012786:G:T	R314I	0.999
6:126012787:A:C	R314S	0.999
6:126012787:A:T	R314S	0.999
6:126013079:T:A	W373R	0.999
6:126013079:T:C	W373R	0.999
6:126021243:G:C	R408T	0.999
6:126021243:G:T	R408M	0.999
6:126021244:G:C	R408S	0.999
6:126021244:G:T	R408S	0.999
6:126021246:G:C	R409P	0.999
6:125999506:G:C	R191T	0.998
6:125999507:A:C	R191S	0.998
6:125999507:A:T	R191S	0.998
6:125999511:T:C	F193L	0.998
6:125999513:T:A	F193L	0.998
6:125999513:T:G	F193L	0.998
6:125999518:G:A	G195E	0.998
6:126008436:G:T	G242W	0.998
6:126011284:A:C	R264S	0.998
6:126011284:A:T	R264S	0.998
6:126011415:A:G	D308G	0.998
6:126012776:T:C	Y311H	0.998
6:126012780:G:A	G312D	0.998
6:125986611:T:C	F21L	0.997
6:125986613:C:A	F21L	0.997
6:125986613:C:G	F21L	0.997

dbSNP variants (sampled 300 via entrez): RS1000036180 (6:126178475 A>G), RS1000041998 (6:126098316 C>G,T), RS1000050108 (6:126223826 C>T), RS1000052199 (6:126225774 T>C), RS1000065482 (6:126257156 G>T), RS1000069262 (6:126024838 A>G), RS1000081740 (6:126249809 T>C), RS1000094647 (6:126097800 A>G), RS1000105193 (6:126114170 A>G), RS1000109155 (6:126053021 T>C), RS1000153322 (6:126046403 T>C), RS1000156519 (6:126231260 C>T), RS1000167743 (6:125992543 A>G), RS1000173943 (6:125985244 G>C), RS1000177424 (6:125996638 A>G)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

10 associations (top):

Study	Trait	p-value
GCST000880_6	Menarche (age at onset)	2.000000e-08
GCST004681_4	Psychosis proneness (hypomanic personality scale and revised physical anhedonia scale)	4.000000e-06
GCST006146_2	Behavioural changes in frontotemporal lobe dementia	7.000000e-06
GCST006661_299	Male-pattern baldness	6.000000e-10
GCST006979_380	Heel bone mineral density	2.000000e-13
GCST012229_115	Hip index	3.000000e-09
GCST90020025_1085	Waist-to-hip ratio adjusted for BMI	2.000000e-11
GCST90020026_138	Hip index	3.000000e-19
GCST90020027_1111	Waist-hip index	7.000000e-13
GCST90020028_545	Hip circumference adjusted for BMI	2.000000e-08

EFO canonical traits (5, from GWAS)

EFO ID	Trait name
EFO:0004703	age at menarche
EFO:0008337	psychosis predisposition measurement
EFO:0009270	heel bone mineral density
EFO:0008039	BMI-adjusted hip circumference
EFO:0007788	BMI-adjusted waist-hip ratio

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

28 total (human), top 28 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression, affects expression	7
Tetrachlorodibenzodioxin	decreases expression	2
Cyclosporine	increases expression	2
aristolochic acid I	increases expression	1
dicrotophos	decreases expression	1
pirinixic acid	affects binding, increases activity, increases expression	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
ferrous chloride	increases expression	1
beta-methylcholine	affects expression	1
di-n-butylphosphoric acid	affects expression	1
perfluorooctane sulfonic acid	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
abrine	increases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
jinfukang	decreases expression	1
Resveratrol	affects cotreatment, increases expression	1
Sunitinib	increases expression	1
Air Pollutants	increases abundance, decreases expression	1
Benzene	increases expression	1
Enzyme Inhibitors	decreases activity, increases O-linked glycosylation	1
Plant Extracts	affects cotreatment, increases expression	1
Quercetin	decreases expression	1
Selenium	decreases expression	1
Smoke	decreases expression, increases abundance	1
Vitamin E	decreases expression	1
Acrylamide	decreases expression	1
Particulate Matter	increases expression	1
Magnetite Nanoparticles	increases expression	1

Clinical trials (associated diseases)

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