TRMT9B

Summary

TRMT9B (tRNA methyltransferase 9B (putative), HGNC:26725) is a protein-coding gene on chromosome 8p22, encoding Probable tRNA methyltransferase 9B (Q9P272). May modify wobble uridines in specific arginine and glutamic acid tRNAs.

Enables tRNA methyltransferase activity. Predicted to be involved in tRNA methylation and tRNA wobble uridine modification. Predicted to be active in cytoplasm and nucleus.

Source: NCBI Gene 57604 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 134 total
• MANE Select transcript: NM_020844

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26725
Approved symbol	TRMT9B
Name	tRNA methyltransferase 9B (putative)
Location	8p22
Locus type	gene with protein product
Status	Approved
Aliases	FLJ36980, TRM9L, hTRM9L
Ensembl gene	ENSG00000250305
Ensembl biotype	protein_coding
OMIM	615666
Entrez	57604

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 10 protein_coding, 2 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000400069, ENST00000447063, ENST00000524591, ENST00000525249, ENST00000528335, ENST00000528753, ENST00000529706, ENST00000529978, ENST00000532376, ENST00000855797, ENST00000966194, ENST00000966195, ENST00000966196

RefSeq mRNA: 2 — MANE Select: NM_020844 NM_001099677, NM_020844

CCDS: CCDS47808

Canonical transcript exons

ENST00000524591 — 5 exons

Exon	Start	End
ENSE00002147239	12945673	12945966
ENSE00002193210	13021008	13029777
ENSE00002294472	12990834	12991031
ENSE00002300522	13006202	13006356
ENSE00002305905	13012684	13012857

Expression profiles

Bgee: expression breadth ubiquitous, 226 present calls, max score 96.23.

FANTOM5 (CAGE): breadth broad, TPM avg 5.4941 / max 588.0670, expressed in 692 samples.

FANTOM5 promoters (25 alternative TSS)

Promoter ID	TPM avg	Samples expressed
87468	1.6210	532
87471	0.8445	181
87466	0.4312	161
87480	0.3564	80
87460	0.3391	60
87470	0.2680	84
87479	0.2551	69
87474	0.2413	104
87472	0.2384	50
87473	0.1426	30

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cerebellar vermis	UBERON:0004720	96.23	gold quality
cerebellar cortex	UBERON:0002129	95.98	gold quality
cerebellar hemisphere	UBERON:0002245	95.92	gold quality
right hemisphere of cerebellum	UBERON:0014890	95.45	gold quality
right lobe of thyroid gland	UBERON:0001119	95.42	gold quality
cerebellum	UBERON:0002037	95.39	gold quality
left lobe of thyroid gland	UBERON:0001120	95.21	gold quality
thyroid gland	UBERON:0002046	94.94	gold quality
endothelial cell	CL:0000115	89.32	gold quality
pons	UBERON:0000988	89.29	gold quality
Brodmann (1909) area 23	UBERON:0013554	89.29	gold quality
buccal mucosa cell	CL:0002336	89.14	gold quality
middle temporal gyrus	UBERON:0002771	87.63	gold quality
cortical plate	UBERON:0005343	87.25	gold quality
primary visual cortex	UBERON:0002436	87.22	gold quality
postcentral gyrus	UBERON:0002581	87.16	gold quality
right uterine tube	UBERON:0001302	86.80	gold quality
parietal lobe	UBERON:0001872	84.67	gold quality
superior frontal gyrus	UBERON:0002661	84.08	gold quality
occipital lobe	UBERON:0002021	83.87	gold quality
right atrium auricular region	UBERON:0006631	82.84	gold quality
mucosa of paranasal sinus	UBERON:0005030	82.53	gold quality
cardiac atrium	UBERON:0002081	81.08	gold quality
ganglionic eminence	UBERON:0004023	81.01	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	80.92	gold quality
metanephros cortex	UBERON:0010533	80.82	gold quality
heart	UBERON:0000948	79.46	gold quality
heart left ventricle	UBERON:0002084	79.36	gold quality
entorhinal cortex	UBERON:0002728	79.22	gold quality
cardiac ventricle	UBERON:0002082	79.17	gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-GEOD-75367	yes	104.58
E-GEOD-93593	yes	7.82
E-GEOD-125970	no	3.53
E-ANND-3	no	2.43

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

291 targeting TRMT9B, 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-4795-3P	100.00	74.62	4024
HSA-MIR-126-5P	100.00	72.71	3180
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-200B-3P	100.00	73.31	2693
HSA-MIR-200C-3P	100.00	73.35	2685
HSA-MIR-429	100.00	73.44	2698
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-4533	100.00	69.48	2758
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-6867-5P	100.00	82.21	3464
HSA-MIR-1252-5P	100.00	69.80	2774
HSA-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-LET-7F-1-3P	100.00	74.02	3928
HSA-MIR-98-3P	100.00	74.08	3907
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-4668-3P	100.00	68.74	2635
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-511-3P	99.99	68.85	1467
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-373-5P	99.98	75.36	4753

Literature-anchored findings (GeneRIF, showing 2)

• Study links hTRM9L and tRNA modifications to inhibition of tumour growth via LIN9 and HIF1-alpha-dependent mechanisms. (PMID:23381944)
• Over-expression of KIAA1456 inhibits the proliferation of HO8910PM ovarian cancer cells and arrests the cell cycle in G1 phase. (PMID:27609572)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Trmt9b	ENSMUSG00000039620
rattus_norvegicus	Trmt9b	ENSRNOG00000011253

Paralogs (2): ALKBH8 (ENSG00000137760), ALKBH6 (ENSG00000239382)

Protein

Protein identifiers

Probable tRNA methyltransferase 9B — Q9P272 (reviewed: Q9P272)

Alternative names: Probable tRNA methyltransferase 9-like protein

All UniProt accessions (4): A0AAA9YHN1, E9PK20, Q9P272, F6XBY7

UniProt curated annotations — full annotation on UniProt →

Function. May modify wobble uridines in specific arginine and glutamic acid tRNAs. Acts as a tumor suppressor by promoting the expression of LIN9.

Tissue specificity. Down-regulated in breast, bladder, colorectal, cervix and testicular carcinomas.

Similarity. Belongs to the methyltransferase superfamily.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9P272-1	1	yes
Q9P272-3	2

RefSeq proteins (2): NP_001093147, NP_065895* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR013216	Methyltransf_11	Domain
IPR029063	SAM-dependent_MTases_sf	Homologous_superfamily
IPR051422	AlkB_tRNA_MeTrf/Diox	Family

Pfam: PF08241

UniProt features (12 total): sequence variant 8, splice variant 2, chain 1, modified residue 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9P272-F1	62.21	0.39

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): 214

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

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

MSigDB gene sets: 127 (showing top): GOBP_TRNA_METABOLIC_PROCESS, GOBP_RNA_METHYLATION, GOBP_RNA_MODIFICATION, GRE_C, SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_UP, GOBP_TRNA_METHYLATION, SCHAEFFER_SOX9_TARGETS_IN_PROSTATE_DEVELOPMENT_UP, AACTTT_UNKNOWN, RFX1_02, GOBP_METHYLATION, RIGGI_EWING_SARCOMA_PROGENITOR_UP, CAGCCTC_MIR4855P, GOBP_TRNA_PROCESSING, REACTOME_METABOLISM_OF_RNA, GOBP_TRNA_MODIFICATION

GO Biological Process (5): tRNA wobble uridine modification (GO:0002098), tRNA modification (GO:0006400), tRNA methylation (GO:0030488), tRNA processing (GO:0008033), methylation (GO:0032259)

GO Molecular Function (6): tRNA binding (GO:0000049), tRNA methyltransferase activity (GO:0008175), S-adenosylmethionine-dependent methyltransferase activity (GO:0008757), tRNA (5-carboxymethyluridine(34)-5-O)-methyltransferase activity (GO:0106335), methyltransferase activity (GO:0008168), transferase activity (GO:0016740)

GO Cellular Component (2): nucleus (GO:0005634), cytoplasm (GO:0005737)

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
tRNA wobble base modification	1
tRNA processing	1
RNA modification	1
RNA methylation	1
tRNA modification	1
RNA processing	1
tRNA metabolic process	1
metabolic process	1
RNA binding	1
RNA methyltransferase activity	1
catalytic activity, acting on a tRNA	1
methyltransferase activity	1
tRNA (uridine) methyltransferase activity	1
transferase activity, transferring one-carbon groups	1
catalytic activity	1
intracellular membrane-bounded organelle	1
intracellular anatomical structure	1
cellular anatomical structure	1

Protein interactions and networks

STRING

1164 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TRMT9B	TRMT112	Q9UI30	690
TRMT9B	TRMT11	Q7Z4G4	607
TRMT9B	CTU1	Q7Z7A3	607
TRMT9B	ELP3	Q9H9T3	606
TRMT9B	TYW2	Q53H54	550
TRMT9B	NSUN2	Q08J23	516
TRMT9B	ALKBH1	Q13686	510
TRMT9B	LIN9	Q5TKA1	486
TRMT9B	TRMT13	Q9NUP7	482
TRMT9B	OR10H2	O60403	474
TRMT9B	FTSJ1	Q9UET6	448
TRMT9B	URM1	Q9BTM9	435
TRMT9B	C8orf48	Q96LL4	434
TRMT9B	LONRF1	Q17RB8	432
TRMT9B	PURG	Q9UJV8	414

IntAct

3 interactions, top by confidence:

A	B	Type	Score
TRMT9B	RPS6KA3	psi-mi:“MI:0914”(association)	0.350
TRMT9B	RUFY3	psi-mi:“MI:0914”(association)	0.350

BioGRID (10): TTC19 (Affinity Capture-MS), ZDHHC17 (Affinity Capture-MS), RUFY3 (Affinity Capture-MS), RPS6KA3 (Affinity Capture-MS), RPS6KA3 (Affinity Capture-MS), RUFY3 (Affinity Capture-MS), KIAA1456 (Affinity Capture-RNA), C9orf156 (Affinity Capture-MS), RUFY3 (Affinity Capture-MS), KIAA1456 (Affinity Capture-RNA)

ESM2 similar proteins: A2AUU0, A3KMI0, E7F654, F1MAB7, P33279, P59114, Q08DH3, Q0P5B2, Q13686, Q28H30, Q3T131, Q3T9Z9, Q49AR2, Q4R8E0, Q5R5W9, Q5R6T6, Q5U2S3, Q5ZLL7, Q62240, Q63185, Q6DTM3, Q6NXH8, Q6NZP1, Q6P1Q9, Q6PAE6, Q6PD74, Q6ZUJ8, Q7SZF1, Q7TNN8, Q7Z3E5, Q8BGC1, Q8BMD7, Q8BMK1, Q8CHK4, Q8K3E5, Q8N6Q8, Q8TE76, Q8W5R2, Q92993, Q96IZ6

Diamond homologs: A0A075D5I4, A0A075D654, A0A075D657, A0A075D6M1, A0A0E0SMA3, A0A1D6NER6, A0A8X8M4T9, A0A8X8M4W6, A0A8X8M501, A0A8X8M505, A1RGE6, A4Y9Y4, A5U866, A9L1I5, B8E5Q5, C3SBU5, C8YTM5, H2E7T7, P0A9H7, P0A9H8, P31049, P46326, P9WPB6, P9WPB7, Q08DH3, Q108P1, Q22993, Q24W96, Q31P90, Q39227, Q4W9V1, Q5N4X9, Q6C2D9, Q6CYB3, Q6ZIK0, Q72HI4, Q7NZ91, Q80WQ4, Q875K1, Q8KZ94

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	111
Likely benign	6
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1485 predictions. Top by Δscore:

Variant	Effect	Δscore
8:12945966:GGTA:G	donor_loss	0.9900
8:12988304:A:G	donor_gain	0.9900
8:12990830:ATAGG:A	acceptor_loss	0.9900
8:12990831:TA:T	acceptor_loss	0.9900
8:12990832:A:AC	acceptor_loss	0.9900
8:12990832:AG:A	acceptor_gain	0.9900
8:12990833:GG:G	acceptor_gain	0.9900
8:13006353:ATAGG:A	donor_loss	0.9900
8:13006354:TAGGT:T	donor_loss	0.9900
8:13006355:AG:A	donor_loss	0.9900
8:13006356:G:T	donor_loss	0.9900
8:13006357:G:A	donor_loss	0.9900
8:13006640:GCAA:G	donor_gain	0.9900
8:13006641:C:T	donor_gain	0.9900
8:13012678:TTATA:T	acceptor_loss	0.9900
8:13012679:TATA:T	acceptor_loss	0.9900
8:13012680:ATAG:A	acceptor_loss	0.9900
8:13012681:TA:T	acceptor_loss	0.9900
8:13012682:A:AC	acceptor_loss	0.9900
8:13012683:G:A	acceptor_loss	0.9900
8:13012683:GGTT:G	acceptor_gain	0.9900
8:13021006:A:AG	acceptor_gain	0.9900
8:13021007:G:GG	acceptor_gain	0.9900
8:12963934:A:AG	donor_gain	0.9800
8:12977376:G:GT	donor_gain	0.9800
8:12990828:T:A	acceptor_gain	0.9800
8:13006200:AGGAT:A	acceptor_gain	0.9800
8:13006201:GGATG:G	acceptor_gain	0.9800
8:13006644:G:GG	donor_gain	0.9800
8:13021007:GTC:G	acceptor_gain	0.9800

AlphaMissense

3029 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
8:13021103:T:A	W142R	0.999
8:13021103:T:C	W142R	0.999
8:13021039:A:C	R120S	0.998
8:13021039:A:T	R120S	0.998
8:13021105:G:C	W142C	0.998
8:13021105:G:T	W142C	0.998
8:13006296:T:A	W32R	0.997
8:13006296:T:C	W32R	0.997
8:13006315:T:C	F38S	0.997
8:13006348:C:A	A49D	0.997
8:13012848:T:C	S107P	0.997
8:13021011:T:A	I111K	0.997
8:13021016:C:G	H113D	0.997
8:13021038:G:C	R120T	0.997
8:13021922:T:C	F415L	0.997
8:13021923:T:C	F415S	0.997
8:13021924:T:A	F415L	0.997
8:13021924:T:G	F415L	0.997
8:13006229:G:C	E9D	0.996
8:13006229:G:T	E9D	0.996
8:13006314:T:C	F38L	0.996
8:13006316:C:A	F38L	0.996
8:13006316:C:G	F38L	0.996
8:13021011:T:G	I111R	0.996
8:13021013:C:G	H112D	0.996
8:13021018:T:A	H113Q	0.996
8:13021018:T:G	H113Q	0.996
8:13021916:C:G	H413D	0.996
8:13012684:G:A	G52D	0.995
8:13012849:C:T	S107F	0.995

dbSNP variants (sampled 300 via entrez): RS1000039370 (8:12986967 T>C,G), RS1000041825 (8:13010522 C>G,T), RS1000057903 (8:12986150 C>G), RS1000108633 (8:12983455 A>G), RS1000151298 (8:12957793 C>A), RS1000169668 (8:13008651 C>G), RS1000170611 (8:12990522 T>G), RS1000193155 (8:13018189 C>T), RS1000200713 (8:13013827 T>C,G), RS1000221864 (8:12965075 T>A,C), RS1000244713 (8:12995061 T>A), RS1000277704 (8:12952452 G>A), RS1000301550 (8:12998843 G>C), RS1000354895 (8:12982515 A>T), RS1000356234 (8:13028348 T>G)

Disease associations

OMIM: gene MIM:615666 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

4 associations (top):

Study	Trait	p-value
GCST002401_4	Post-traumatic stress disorder	5.000000e-06
GCST002415_1	Colorectal cancer (diet interaction)	2.000000e-06
GCST003400_24	Type 2 diabetes	4.000000e-06
GCST004744_44	Lung adenocarcinoma	6.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0008111	diet measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression	4
trichostatin A	affects cotreatment, increases expression	2
sodium arsenite	affects methylation, decreases expression	2
Benzo(a)pyrene	affects methylation, increases methylation	2
Aflatoxin B1	decreases expression, decreases methylation	2
fluorene-9-bisphenol	increases expression	1
sotorasib	affects cotreatment, increases expression	1
bufotalin	decreases expression	1
aflatoxin B2	decreases methylation	1
4-nonylphenol	affects cotreatment, increases expression	1
4-tert-octylphenol	affects cotreatment, increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
abrine	decreases expression	1
dorsomorphin	increases expression, affects cotreatment	1
trametinib	affects cotreatment, increases expression	1
MT19c compound	decreases expression	1
NVP-BKM120	affects cotreatment, increases expression	1
Acetaminophen	decreases expression	1
Arsenic	affects methylation	1
Carbamazepine	affects expression	1
Diethylhexyl Phthalate	decreases expression	1
Doxorubicin	decreases expression	1
Phthalic Acids	increases methylation	1
Thiram	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Tretinoin	increases expression	1
Triclosan	decreases expression	1
Antirheumatic Agents	increases expression	1
Okadaic Acid	decreases expression	1
Acrylamide	decreases expression	1

Clinical trials (associated diseases)

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