TRMT10B

Summary

TRMT10B (tRNA methyltransferase 10B, HGNC:26454) is a protein-coding gene on chromosome 9p13.2, encoding tRNA methyltransferase 10 homolog B (Q6PF06). S-adenosyl-L-methionine-dependent guanine N(1)-methyltransferase that catalyzes the formation of N(1)-methylguanine at position 9 (m1G9) in tRNAs.

Enables tRNA (guanosine(9)-N1)-methyltransferase activity. Involved in protein insertion into mitochondrial inner membrane. Located in cytosol and mitochondrial inner membrane. Part of TIM22 mitochondrial import inner membrane insertion complex.

Source: NCBI Gene 158234 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 60 total
• MANE Select transcript: NM_144964

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26454
Approved symbol	TRMT10B
Name	tRNA methyltransferase 10B
Location	9p13.2
Locus type	gene with protein product
Status	Approved
Aliases	FLJ31455, bA3J10.9
Ensembl gene	ENSG00000165275
Ensembl biotype	protein_coding
OMIM	620957
Entrez	158234

Gene structure

Transcript identifiers

Ensembl transcripts: 15 — 10 protein_coding, 4 nonsense_mediated_decay, 1 retained_intron

ENST00000297994, ENST00000377753, ENST00000377754, ENST00000488673, ENST00000509577, ENST00000537016, ENST00000537911, ENST00000538370, ENST00000540616, ENST00000857926, ENST00000857927, ENST00000913190, ENST00000913191, ENST00000913192, ENST00000913193

RefSeq mRNA: 6 — MANE Select: NM_144964 NM_001286950, NM_001286951, NM_001286952, NM_001286953, NM_001286954, NM_144964

CCDS: CCDS43804, CCDS69598, CCDS69600, CCDS69601

Canonical transcript exons

ENST00000297994 — 9 exons

Exon	Start	End
ENSE00001091800	37762577	37762685
ENSE00001091804	37763629	37763753
ENSE00001475021	37777601	37778972
ENSE00003483205	37770672	37770739
ENSE00003526515	37761903	37762117
ENSE00003548862	37776282	37776405
ENSE00003561681	37768076	37768228
ENSE00003599504	37769941	37770019
ENSE00003846365	37753805	37753852

Expression profiles

Bgee: expression breadth ubiquitous, 166 present calls, max score 85.91.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 3.8842 / max 66.4794, expressed in 1544 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
96746	3.8842	1544

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right uterine tube	UBERON:0001302	85.91	gold quality
left ovary	UBERON:0002119	85.82	gold quality
right ovary	UBERON:0002118	85.66	gold quality
monocyte	CL:0000576	85.51	gold quality
calcaneal tendon	UBERON:0003701	85.38	gold quality
leukocyte	CL:0000738	85.11	gold quality
endocervix	UBERON:0000458	85.09	gold quality
muscle layer of sigmoid colon	UBERON:0035805	84.89	gold quality
body of uterus	UBERON:0009853	84.76	gold quality
body of pancreas	UBERON:0001150	84.49	gold quality
granulocyte	CL:0000094	84.42	gold quality
tibial nerve	UBERON:0001323	84.33	gold quality
lower esophagus muscularis layer	UBERON:0035833	84.32	gold quality
lower esophagus	UBERON:0013473	84.31	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	84.23	gold quality
mucosa of stomach	UBERON:0001199	83.83	gold quality
right lobe of thyroid gland	UBERON:0001119	83.81	gold quality
cerebellar hemisphere	UBERON:0002245	83.79	gold quality
tibial artery	UBERON:0007610	83.79	gold quality
right adrenal gland	UBERON:0001233	83.78	gold quality
popliteal artery	UBERON:0002250	83.78	gold quality
ectocervix	UBERON:0012249	83.69	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	83.68	gold quality
cerebellar cortex	UBERON:0002129	83.59	gold quality
right adrenal gland cortex	UBERON:0035827	83.59	gold quality
smooth muscle tissue	UBERON:0001135	83.54	gold quality
left lobe of thyroid gland	UBERON:0001120	83.42	gold quality
right hemisphere of cerebellum	UBERON:0014890	83.26	gold quality
adrenal tissue	UBERON:0018303	83.26	gold quality
descending thoracic aorta	UBERON:0002345	83.16	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.78
E-MTAB-6386	no	158.06
E-MTAB-6142	no	97.48

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

51 targeting TRMT10B, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-4476	100.00	68.18	2030
HSA-MIR-6876-5P	100.00	67.68	2126
HSA-MIR-4533	100.00	69.48	2758
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-590-3P	99.96	74.34	6478
HSA-LET-7C-3P	99.95	73.42	2862
HSA-MIR-30A-3P	99.87	69.74	2928
HSA-MIR-30D-3P	99.87	69.92	2917
HSA-MIR-30E-3P	99.87	69.68	2942
HSA-MIR-4739	99.84	65.25	1832
HSA-MIR-1321	99.84	65.30	1811
HSA-MIR-4756-5P	99.84	64.98	1809
HSA-MIR-4719	99.73	72.10	3329
HSA-MIR-4422	99.72	72.07	2908
HSA-MIR-5580-3P	99.70	69.41	2052
HSA-MIR-3975	99.62	65.97	697
HSA-MIR-1249-5P	99.61	66.55	2049
HSA-MIR-6797-5P	99.61	66.55	2084
HSA-MIR-6832-5P	99.58	64.82	1132
HSA-MIR-7106-5P	99.53	67.47	3574
HSA-MIR-4441	99.49	66.56	3216
HSA-MIR-4251	99.40	69.19	3363
HSA-MIR-3606-5P	99.31	69.67	1168
HSA-MIR-504-3P	99.30	67.18	1745
HSA-MIR-10522-5P	99.26	68.50	2087
HSA-MIR-7151-3P	99.04	69.72	2370
HSA-MIR-4270	99.02	66.26	1987
HSA-MIR-6871-5P	98.90	66.67	671
HSA-MIR-1304-5P	98.90	68.58	1054

Literature-anchored findings (GeneRIF, showing 2)

• demonstrate that human TRMT10A (hTRMT10A) and human TRMT10B (hTRMT10B) are not biochemically redundant (PMID:31292261)
• Functional characterization of the human tRNA methyltransferases TRMT10A and TRMT10B. (PMID:32392304)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	trmt10b	ENSDARG00000060176
mus_musculus	Trmt10b	ENSMUSG00000035601
rattus_norvegicus	Trmt10b	ENSRNOG00000012454

Paralogs (2): TRMT10A (ENSG00000145331), TRMT10C (ENSG00000174173)

Protein

Protein identifiers

tRNA methyltransferase 10 homolog B — Q6PF06 (reviewed: Q6PF06)

Alternative names: RNA (guanine-9-)-methyltransferase domain-containing protein 3, tRNA (guanine(9)-N(1))-methyltransferase TRMT10B

All UniProt accessions (4): Q6PF06, F5H380, F5H4N3, F5H598

UniProt curated annotations — full annotation on UniProt →

Function. S-adenosyl-L-methionine-dependent guanine N(1)-methyltransferase that catalyzes the formation of N(1)-methylguanine at position 9 (m1G9) in tRNAs. Probably not able to catalyze formation of N(1)-methyladenine at position 9 (m1A9) in tRNAs.

Similarity. Belongs to the class IV-like SAM-binding methyltransferase superfamily. TRM10 family.

Isoforms (5)

UniProt ID	Names	Canonical?
Q6PF06-1	1	yes
Q6PF06-2	2
Q6PF06-5	5
Q6PF06-3	3
Q6PF06-4	4

RefSeq proteins (6): NP_001273879, NP_001273880, NP_001273881, NP_001273882, NP_001273883, NP_659401* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR007356	tRNA_m1G_MeTrfase_euk	Family
IPR028564	MT_TRM10-typ	Domain
IPR038459	MT_TRM10-typ_sf	Homologous_superfamily
IPR047911	Trm10_B_MTase_dom	Domain

Enzyme classification (BRENDA):

• EC 2.1.1.218 — tRNA (adenine9-N1)-methyltransferase (BRENDA: 4 organisms, 27 substrates, 0 inhibitors, 2 Km, 2 kcat entries)

Substrate kinetics (BRENDA)

2 substrates with measured Km, best-characterized 2. Km ranges are aggregated across organisms/conditions.

Substrate	Km (mM)	Measurements
ADENINE9 IN TRNAPHE	—	0
ADENINE9 IN TRNATHR	—	0

Catalyzed reactions (Rhea), 1 shown:

• guanosine(9) in tRNA + S-adenosyl-L-methionine = N(1)-methylguanosine(9) in tRNA + S-adenosyl-L-homocysteine + H(+) (RHEA:43156)

UniProt features (13 total): splice variant 6, sequence variant 2, chain 1, domain 1, sequence conflict 1, region of interest 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6PF06-F1	80.88	0.58

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 103 (showing top): STARK_PREFRONTAL_CORTEX_22Q11_DELETION_DN, GOBP_TRNA_METABOLIC_PROCESS, GOBP_ESTABLISHMENT_OF_PROTEIN_LOCALIZATION_TO_ORGANELLE, GOBP_RNA_METHYLATION, AACWWCAANK_UNKNOWN, GOBP_RNA_MODIFICATION, GOBP_INNER_MITOCHONDRIAL_MEMBRANE_ORGANIZATION, chr9p13, GOBP_ESTABLISHMENT_OF_PROTEIN_LOCALIZATION_TO_MEMBRANE, GOBP_TRNA_METHYLATION, GOCC_MITOCHONDRIAL_ENVELOPE, GOBP_PROTEIN_LOCALIZATION_TO_ORGANELLE, GOBP_MEMBRANE_ORGANIZATION, GOBP_PROTEIN_LOCALIZATION_TO_MITOCHONDRION, GOBP_LOCALIZATION_WITHIN_MEMBRANE

GO Biological Process (3): tRNA N1-guanine methylation (GO:0002939), protein insertion into mitochondrial inner membrane (GO:0045039), methylation (GO:0032259)

GO Molecular Function (5): tRNA binding (GO:0000049), tRNA (guanosine(9)-N1)-methyltransferase activity (GO:0052905), protein binding (GO:0005515), methyltransferase activity (GO:0008168), transferase activity (GO:0016740)

GO Cellular Component (5): nucleus (GO:0005634), nucleoplasm (GO:0005654), mitochondrial inner membrane (GO:0005743), cytosol (GO:0005829), TIM22 mitochondrial import inner membrane insertion complex (GO:0042721)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
tRNA methylation	1
inner mitochondrial membrane organization	1
mitochondrial protein import pathway	1
metabolic process	1
RNA binding	1
tRNA (guanine) methyltransferase activity	1
binding	1
transferase activity, transferring one-carbon groups	1
catalytic activity	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
organelle inner membrane	1
mitochondrial membrane	1
cytoplasm	1
inner mitochondrial membrane protein complex	1

Protein interactions and networks

STRING

1292 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TRMT10B	TRMT5	Q32P41	709
TRMT10B	METTL6	Q8TCB7	608
TRMT10B	HSD17B10	Q99714	596
TRMT10B	METTL8	Q9H825	590
TRMT10B	TRMT6	Q9UJA5	570
TRMT10B	METTL2A	Q96IZ6	564
TRMT10B	WDR4	P57081	557
TRMT10B	METTL2B	Q6P1Q9	525
TRMT10B	TRMT11	Q7Z4G4	512
TRMT10B	TRMT61B	Q9BVS5	493
TRMT10B	PRORP	O15091	488
TRMT10B	TTLL11	Q8NHH1	483
TRMT10B	TRMT1	Q9NXH9	472
TRMT10B	TRMT61A	Q96FX7	463
TRMT10B	PRR30	Q53SZ7	461

IntAct

9 interactions, top by confidence:

A	B	Type	Score
OTX2	TRMT10B	psi-mi:“MI:0915”(physical association)	0.560
TRMT10B	MRPS14	psi-mi:“MI:0914”(association)	0.530
TRMT10B	NPM1	psi-mi:“MI:0915”(physical association)	0.400
TRMT10B	MEIS1	psi-mi:“MI:0915”(physical association)	0.370
TRMT10B	RPS27A	psi-mi:“MI:0914”(association)	0.350
TRMT10B	OTX2	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (96): RPL26L1 (Affinity Capture-MS), MRPS9 (Affinity Capture-MS), MRPS26 (Affinity Capture-MS), PTCD3 (Affinity Capture-MS), MRPS23 (Affinity Capture-MS), MRPS27 (Affinity Capture-MS), MRPS18B (Affinity Capture-MS), MRPS10 (Affinity Capture-MS), MRPS34 (Affinity Capture-MS), DAP3 (Affinity Capture-MS), NOA1 (Affinity Capture-MS), MRPS28 (Affinity Capture-MS), MRPS31 (Affinity Capture-MS), MRPS18C (Affinity Capture-MS), MRPS5 (Affinity Capture-MS)

ESM2 similar proteins: A1A5Q7, A2RUS2, A4PCD4, A5PKL6, A6QPR9, E1BVR9, E9PYK3, F1ND48, O02789, O57486, O94952, P04053, P06526, P09838, P36195, P42118, Q08DP1, Q0VCL9, Q3U3W5, Q3UVV9, Q4KM51, Q4R6Y8, Q502W6, Q5JPI3, Q5R5S1, Q5RJK3, Q5RL51, Q5SSK3, Q66H33, Q66IH9, Q67VC8, Q68D06, Q6PF06, Q7SXA9, Q7Z7L1, Q8BGG7, Q8BIW1, Q8IXQ6, Q8NEC7, Q8VDH1

Diamond homologs: A4IHS0, O14214, Q08BM0, Q08DP1, Q2KI45, Q3MHI8, Q3UFY8, Q4I8X0, Q4KLI2, Q4WXA1, Q59Q39, Q5B8X0, Q5U2R4, Q6C1W9, Q6PF06, Q7JUX9, Q7L0Y3, Q8C1Z8, Q8TBZ6, Q9VR56, P0CS10, P0CS11, Q12400, Q5RJK3, Q66JJ4, Q6BWG3, Q6CUM6, Q6FQB2, Q75A17, Q9D075

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
TRMT10B	“form complex”	“TIM22 complex”	binding

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	45
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1796 predictions. Top by Δscore:

Variant	Effect	Δscore
9:37762529:T:A	acceptor_gain	1.0000
9:37768074:A:AG	acceptor_gain	1.0000
9:37768075:G:GG	acceptor_gain	1.0000
9:37768226:CTGGT:C	donor_loss	1.0000
9:37768227:TGGT:T	donor_loss	1.0000
9:37768228:GGTA:G	donor_loss	1.0000
9:37768229:G:GG	donor_gain	1.0000
9:37768229:GT:G	donor_loss	1.0000
9:37768230:T:A	donor_loss	1.0000
9:37769939:A:AG	acceptor_gain	1.0000
9:37769940:G:GG	acceptor_gain	1.0000
9:37769940:GTTA:G	acceptor_gain	1.0000
9:37770670:A:AG	acceptor_gain	1.0000
9:37770671:G:GA	acceptor_gain	1.0000
9:37770671:GCT:G	acceptor_gain	1.0000
9:37770738:AGGTA:A	donor_loss	1.0000
9:37770739:GGTA:G	donor_loss	1.0000
9:37770740:G:GG	donor_gain	1.0000
9:37776280:A:AG	acceptor_gain	1.0000
9:37776281:G:GG	acceptor_gain	1.0000
9:37761901:A:AG	acceptor_gain	0.9900
9:37761901:AGTCT:A	acceptor_gain	0.9900
9:37761902:G:GA	acceptor_gain	0.9900
9:37761902:GTCT:G	acceptor_gain	0.9900
9:37761902:GTCTG:G	acceptor_gain	0.9900
9:37762530:G:A	acceptor_gain	0.9900
9:37762564:T:TA	acceptor_gain	0.9900
9:37762565:G:A	acceptor_gain	0.9900
9:37762569:A:AG	acceptor_gain	0.9900
9:37763860:AAACT:A	donor_gain	0.9900

AlphaMissense

2066 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
9:37776331:T:C	L257S	0.997
9:37777639:T:A	W295R	0.996
9:37777639:T:C	W295R	0.996
9:37768089:T:C	L145P	0.994
9:37769999:T:C	L211P	0.994
9:37768092:C:A	A146D	0.993
9:37777641:G:C	W295C	0.993
9:37777641:G:T	W295C	0.993
9:37768193:T:C	C180R	0.992
9:37768214:T:C	F187L	0.992
9:37768216:T:A	F187L	0.992
9:37768216:T:G	F187L	0.992
9:37770724:T:A	D235E	0.992
9:37770724:T:G	D235E	0.992
9:37769999:T:A	L211Q	0.991
9:37770714:G:A	G232E	0.991
9:37776328:G:C	R256P	0.991
9:37777613:T:C	L286P	0.990
9:37768116:G:A	G154D	0.989
9:37776324:G:C	A255P	0.989
9:37776334:C:A	P258Q	0.989
9:37768215:T:C	F187S	0.988
9:37777652:T:C	L299S	0.988
9:37769995:T:G	Y210D	0.987
9:37770701:T:G	Y228D	0.987
9:37770722:G:C	D235H	0.987
9:37770723:A:T	D235V	0.987
9:37763715:T:C	C128R	0.986
9:37770717:T:C	L233P	0.986
9:37777648:G:C	A298P	0.986

dbSNP variants (sampled 300 via entrez): RS1000164808 (9:37769074 G>A), RS1000168924 (9:37753146 T>C), RS1000194480 (9:37776974 A>AC), RS1000336017 (9:37751745 G>A), RS1000450292 (9:37753075 C>G,T), RS1000521384 (9:37762859 G>A,T), RS1000888856 (9:37775552 A>G), RS1000939467 (9:37753662 A>G,T), RS1001038137 (9:37756592 G>T), RS1001194500 (9:37750925 G>C), RS1001230117 (9:37753535 C>T), RS1001470282 (9:37753452 T>C,G), RS1001526599 (9:37764422 C>T), RS1001536417 (9:37764631 C>A), RS1001679295 (9:37753922 C>T)

Disease associations

OMIM: gene MIM:620957 | 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)

CTD chemical–gene interactions

21 total (human), top 21 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression	2
Acetaminophen	increases expression	2
Valproic Acid	affects cotreatment, decreases expression	2
Particulate Matter	decreases reaction, increases expression	2
CGP 52608	affects binding, increases reaction	1
perfluoro-n-nonanoic acid	increases expression	1
2-palmitoylglycerol	increases 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
2-methyl-2H-pyrazole-3-carboxylic acid (2-methyl-4-o-tolylazophenyl)amide	decreases reaction, increases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
(+)-JQ1 compound	decreases expression	1
Resveratrol	affects cotreatment, increases expression	1
Temozolomide	increases expression	1
Sunitinib	increases expression	1
Fulvestrant	increases methylation	1
Amiodarone	increases expression	1
Vehicle Emissions	decreases reaction, increases expression	1
Methyl Methanesulfonate	increases expression	1
Plant Extracts	affects cotreatment, increases expression	1
Copper Sulfate	decreases expression	1

Cellosaurus cell lines

2 cell lines: 2 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_TU74	HAP1 TRMT10B (-) 1	Cancer cell line	Male
CVCL_TU75	HAP1 TRMT10B (-) 2	Cancer cell line	Male

Clinical trials (associated diseases)

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