TRMT13

Summary

TRMT13 (tRNA methyltransferase 13, HGNC:25502) is a protein-coding gene on chromosome 1p21.2, encoding tRNA:m(4)X modification enzyme TRM13 homolog (Q9NUP7). tRNA methylase which 2’-O-methylates cytidine(4) in tRNA(Pro) and tRNA(Gly)(GCC), and adenosine(4) in tRNA(His).

Predicted to enable tRNA methyltransferase activity. Predicted to be involved in tRNA methylation.

Source: NCBI Gene 54482 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 64 total
• MANE Select transcript: NM_019083

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25502
Approved symbol	TRMT13
Name	tRNA methyltransferase 13
Location	1p21.2
Locus type	gene with protein product
Status	Approved
Aliases	FLJ10287, FLJ11219, hTrmt13
Ensembl gene	ENSG00000122435
Ensembl biotype	protein_coding
Entrez	54482

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 4 protein_coding, 1 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000370139, ENST00000370141, ENST00000370143, ENST00000482437, ENST00000493651, ENST00000962881

RefSeq mRNA: 7 — MANE Select: NM_019083 NM_001393409, NM_001393410, NM_001393411, NM_001393412, NM_001393413, NM_001393414, NM_019083

CCDS: CCDS765

Canonical transcript exons

ENST00000370141 — 11 exons

Exon	Start	End
ENSE00000831276	100136882	100136928
ENSE00000831277	100137019	100137085
ENSE00000831278	100139649	100139711
ENSE00000831279	100140182	100140251
ENSE00000831284	100147894	100148326
ENSE00000957842	100140852	100141019
ENSE00001238296	100144069	100144143
ENSE00001238346	100140408	100140514
ENSE00001451926	100148625	100150496
ENSE00001842823	100133163	100133315
ENSE00003609814	100143137	100143209

Expression profiles

Bgee: expression breadth ubiquitous, 272 present calls, max score 91.73.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 16.8580 / max 315.7795, expressed in 1764 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
4216	15.4474	1755
4217	1.4106	730

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
secondary oocyte	CL:0000655	91.73	gold quality
calcaneal tendon	UBERON:0003701	91.54	gold quality
corpus callosum	UBERON:0002336	89.13	gold quality
body of pancreas	UBERON:0001150	88.29	gold quality
right uterine tube	UBERON:0001302	87.39	gold quality
right ovary	UBERON:0002118	87.33	gold quality
left ovary	UBERON:0002119	87.09	gold quality
lymph node	UBERON:0000029	86.96	gold quality
rectum	UBERON:0001052	86.66	gold quality
adrenal tissue	UBERON:0018303	86.55	gold quality
sural nerve	UBERON:0015488	86.29	gold quality
ovary	UBERON:0000992	86.23	gold quality
body of uterus	UBERON:0009853	85.92	gold quality
tibial nerve	UBERON:0001323	85.86	gold quality
buccal mucosa cell	CL:0002336	85.85	gold quality
oocyte	CL:0000023	85.60	gold quality
endocervix	UBERON:0000458	85.56	gold quality
vermiform appendix	UBERON:0001154	85.50	gold quality
hindlimb stylopod muscle	UBERON:0004252	85.39	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	85.19	gold quality
endometrium	UBERON:0001295	85.08	gold quality
caput epididymis	UBERON:0004358	84.99	gold quality
vagina	UBERON:0000996	84.75	gold quality
inferior vagus X ganglion	UBERON:0005363	84.71	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	84.65	gold quality
gastrocnemius	UBERON:0001388	84.64	gold quality
ectocervix	UBERON:0012249	84.61	gold quality
muscle of leg	UBERON:0001383	84.58	gold quality
tendon	UBERON:0000043	84.52	gold quality
minor salivary gland	UBERON:0001830	84.43	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.32

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): E2F4

miRNA regulators (miRDB)

117 targeting TRMT13, 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-5692A	100.00	74.40	6850
HSA-MIR-12118	100.00	65.88	1270
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-4500	99.99	72.72	2367
HSA-LET-7F-5P	99.98	72.56	1784
HSA-MIR-6891-5P	99.98	66.53	1372
HSA-LET-7A-5P	99.98	72.29	1790
HSA-LET-7B-5P	99.98	72.31	1790
HSA-LET-7C-5P	99.98	72.29	1790
HSA-LET-7E-5P	99.98	72.29	1790
HSA-LET-7G-5P	99.98	72.37	1784
HSA-LET-7I-5P	99.98	72.37	1788
HSA-MIR-98-5P	99.98	72.33	1787
HSA-MIR-4482-3P	99.98	72.50	3147
HSA-MIR-3173-3P	99.98	66.49	1217
HSA-MIR-607	99.97	73.62	5593
HSA-LET-7D-5P	99.96	71.76	1632
HSA-MIR-4458	99.96	71.64	1650
HSA-MIR-548AT-5P	99.96	70.83	2666
HSA-MIR-9983-3P	99.94	71.48	3631
HSA-MIR-218-5P	99.93	72.22	2103
HSA-MIR-205-3P	99.92	69.92	3165
HSA-MIR-95-5P	99.89	72.17	3973
HSA-MIR-5582-3P	99.86	72.48	4221
HSA-MIR-5010-3P	99.83	70.60	2357
HSA-MIR-944	99.82	70.85	3042
HSA-MIR-4307	99.82	70.45	3374
HSA-MIR-636	99.80	69.58	1500

Literature-anchored findings (GeneRIF, showing 1)

• A dual role of human tRNA methyltransferase hTrmt13 in regulating translation and transcription. (PMID:34850409)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	trmt13	ENSDARG00000102846
mus_musculus	Trmt13	ENSMUSG00000033439
rattus_norvegicus	Trmt13	ENSRNOG00000015140
drosophila_melanogaster	CG18048	FBGN0037435
caenorhabditis_elegans		WBGENE00013026

Protein

Protein identifiers

tRNA:m(4)X modification enzyme TRM13 homolog — Q9NUP7 (reviewed: Q9NUP7)

Alternative names: Coiled-coil domain-containing protein 76

All UniProt accessions (3): Q9NUP7, Q5VVK9, Q5VVL2

UniProt curated annotations — full annotation on UniProt →

Function. tRNA methylase which 2’-O-methylates cytidine(4) in tRNA(Pro) and tRNA(Gly)(GCC), and adenosine(4) in tRNA(His).

Similarity. Belongs to the methyltransferase TRM13 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9NUP7-1	1	yes
Q9NUP7-2	2

RefSeq proteins (7): NP_001380338, NP_001380339, NP_001380340, NP_001380341, NP_001380342, NP_001380343, NP_061956* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR007871	Methyltransferase_TRM13	Domain
IPR021721	Znf_CCCH-type_TRM13	Domain
IPR022776	TRM13/UPF0224_CHHC_Znf_dom	Domain
IPR039044	Trm13	Family

Pfam: PF05206, PF05253, PF11722

Catalyzed reactions (Rhea), 3 shown:

• cytidine(4) in tRNA(Pro) + S-adenosyl-L-methionine = 2’-O-methylcytidine(4) in tRNA(Pro) + S-adenosyl-L-homocysteine + H(+) (RHEA:32767)
• cytidine(4) in tRNA(Gly)(GCC) + S-adenosyl-L-methionine = 2’-O-methylcytidine(4) in tRNA(Gly)(GCC) + S-adenosyl-L-homocysteine + H(+) (RHEA:43192)
• adenosine(4) in tRNA(His) + S-adenosyl-L-methionine = 2’-O-methyladenosine(4) in tRNA(His) + S-adenosyl-L-homocysteine + H(+) (RHEA:43196)

UniProt features (14 total): binding site 4, splice variant 2, initiator methionine 1, chain 1, sequence variant 1, sequence conflict 1, zinc finger region 1, region of interest 1, coiled-coil region 1, modified residue 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9NUP7-F1	79.51	0.54

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 (4): 59; 65; 75; 79

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: 152 (showing top): E2F_Q4, E2F_Q4_01, E2F4DP1_01, CMYB_01, GOBP_TRNA_METABOLIC_PROCESS, GOBP_RNA_METHYLATION, E2F1DP1_01, E2F_Q3, E2F1DP2_01, GOBP_RNA_MODIFICATION, GOBP_TRNA_METHYLATION, AACTTT_UNKNOWN, E2F1_Q3, E2F_Q6_01, DANG_BOUND_BY_MYC

GO Biological Process (3): tRNA methylation (GO:0030488), tRNA processing (GO:0008033), methylation (GO:0032259)

GO Molecular Function (6): tRNA methyltransferase activity (GO:0008175), zinc ion binding (GO:0008270), obsolete tRNA 2’-O-methyltransferase activity (GO:0106050), methyltransferase activity (GO:0008168), transferase activity (GO:0016740), metal ion binding (GO:0046872)

GO Cellular Component (0):

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
RNA methylation	1
tRNA modification	1
RNA processing	1
tRNA metabolic process	1
metabolic process	1
RNA methyltransferase activity	1
catalytic activity, acting on a tRNA	1
transition metal ion binding	1
transferase activity, transferring one-carbon groups	1
catalytic activity	1
cation binding	1

Protein interactions and networks

STRING

1114 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TRMT13	LRRC39	Q96DD0	601
TRMT13	SAYSD1	Q9NPB0	566
TRMT13	TPGS2	Q68CL5	550
TRMT13	TRMT44	Q8IYL2	543
TRMT13	C5orf22	Q49AR2	541
TRMT13	DBT	P11182	536
TRMT13	RTCA	O00442	512
TRMT13	DIMT1	Q9UNQ2	507
TRMT13	TRMT11	Q7Z4G4	499
TRMT13	CMTR2	Q8IYT2	486
TRMT13	TRMT9B	Q9P272	482
TRMT13	TRMT10C	Q7L0Y3	472
TRMT13	PURG	Q9UJV8	429
TRMT13	PIGH	Q14442	423
TRMT13	METTL15	A6NJ78	423

IntAct

136 interactions, top by confidence:

A	B	Type	Score
TRMT13	STAG1	psi-mi:“MI:0914”(association)	0.530
TRMT13	DLG3	psi-mi:“MI:0407”(direct interaction)	0.440
TRMT13	TIAM2	psi-mi:“MI:0407”(direct interaction)	0.440
TRMT13	APBA3	psi-mi:“MI:0407”(direct interaction)	0.440
RHPN1	TRMT13	psi-mi:“MI:0407”(direct interaction)	0.440
TRMT13	SNX27	psi-mi:“MI:0407”(direct interaction)	0.440
TRMT13	MAGI3	psi-mi:“MI:0407”(direct interaction)	0.440
TRMT13	GRID2IP	psi-mi:“MI:0407”(direct interaction)	0.440
TRMT13	MAGI2	psi-mi:“MI:0407”(direct interaction)	0.440
TRMT13	SNTG2	psi-mi:“MI:0407”(direct interaction)	0.440
TRMT13	DLG4	psi-mi:“MI:0407”(direct interaction)	0.440
TRMT13	GOPC	psi-mi:“MI:0407”(direct interaction)	0.440
TRMT13	GRIP2	psi-mi:“MI:0407”(direct interaction)	0.440
TRMT13	PICK1	psi-mi:“MI:0407”(direct interaction)	0.440
TRMT13	PDZD2	psi-mi:“MI:0407”(direct interaction)	0.440
TRMT13	TJP1	psi-mi:“MI:0407”(direct interaction)	0.440
TRMT13	WHRN	psi-mi:“MI:0407”(direct interaction)	0.440
TRMT13	IL16	psi-mi:“MI:0407”(direct interaction)	0.440
MAGI2	TRMT13	psi-mi:“MI:0407”(direct interaction)	0.440
TRMT13	PDZRN3	psi-mi:“MI:0407”(direct interaction)	0.440
CARD11	TRMT13	psi-mi:“MI:0407”(direct interaction)	0.440
TRMT13	FRMPD4	psi-mi:“MI:0407”(direct interaction)	0.440
TRMT13	HTRA2	psi-mi:“MI:0407”(direct interaction)	0.440
TRMT13	HTRA4	psi-mi:“MI:0407”(direct interaction)	0.440
TRMT13	ARHGAP21	psi-mi:“MI:0407”(direct interaction)	0.440

BioGRID (14): TRMT13 (Affinity Capture-MS), STAG1 (Affinity Capture-MS), OSER1 (Affinity Capture-MS), TRMT13 (Affinity Capture-RNA), TRMT13 (Proximity Label-MS), TRMT13 (Affinity Capture-MS), OSER1 (Affinity Capture-MS), STAG1 (Affinity Capture-MS), AGO1 (Affinity Capture-MS), TRMT13 (Affinity Capture-MS), TRMT13 (Proximity Label-MS), TRMT13 (Proximity Label-MS), TRMT13 (Proximity Label-MS), TRMT13 (Affinity Capture-RNA)

ESM2 similar proteins: A0A0R4IB93, A0JMU5, A1A4L5, A2PYH4, A2RUV5, B3M1E1, B3P4N5, B4GZ20, B4HJC0, B4KA23, B4LVS8, B4NKI9, B4PVH6, B4QVW6, B6DMK2, D3Z4R1, O75417, O93530, O94830, Q07G10, Q0P5B2, Q15326, Q28ES8, Q29B63, Q4KLT3, Q4R6F3, Q5M8E6, Q5ZIJ9, Q5ZJM3, Q6GQ76, Q6NRS1, Q6NTR1, Q6P1Q9, Q6ZPR6, Q7ZU90, Q80Y20, Q84MA1, Q8BMK1, Q8BYH3, Q8MNT9

Diamond homologs: Q8BYH3, Q9NUP7, A3LXS6, A7TSF4, Q12383, Q6BP10, Q6C4F8, Q9UTH1

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 88 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:

Pathway	Partners	Fold	FDR
Ras activation upon Ca2+ influx through NMDA receptor	5	52.9×	1e-06
Unblocking of NMDA receptors, glutamate binding and activation	5	50.4×	1e-06
Negative regulation of NMDA receptor-mediated neuronal transmission	5	50.4×	1e-06
Assembly and cell surface presentation of NMDA receptors	10	47.0×	7e-13
Dopamine Neurotransmitter Release Cycle	5	46.0×	2e-06
Long-term potentiation	5	44.1×	2e-06
Neurexins and neuroligins	11	40.1×	4e-13
Protein-protein interactions at synapses	7	34.4×	7e-08

GO biological processes:

GO term	Partners	Fold	FDR
establishment or maintenance of epithelial cell apical/basal polarity	11	76.1×	4e-16
protein localization to synapse	6	54.7×	1e-07
receptor clustering	7	52.0×	1e-08
regulation of postsynaptic membrane neurotransmitter receptor levels	7	41.3×	5e-08
protein-containing complex assembly	9	12.2×	3e-06
cell-cell adhesion	10	12.1×	8e-07
regulation of small GTPase mediated signal transduction	5	8.6×	6e-03
chemical synaptic transmission	7	6.4×	3e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	56
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1865 predictions. Top by Δscore:

Variant	Effect	Δscore
1:100133347:GAAA:G	donor_gain	1.0000
1:100133350:A:AG	donor_gain	1.0000
1:100136876:TATTA:T	acceptor_loss	1.0000
1:100136878:TTAG:T	acceptor_loss	1.0000
1:100136880:AGG:A	acceptor_loss	1.0000
1:100136881:G:GA	acceptor_loss	1.0000
1:100136924:AAACA:A	donor_gain	1.0000
1:100136925:AACA:A	donor_gain	1.0000
1:100136926:ACA:A	donor_gain	1.0000
1:100136927:CA:C	donor_gain	1.0000
1:100136927:CAGT:C	donor_loss	1.0000
1:100136928:AGTA:A	donor_loss	1.0000
1:100136929:G:GG	donor_gain	1.0000
1:100136929:GT:G	donor_loss	1.0000
1:100137017:A:AG	acceptor_gain	1.0000
1:100137018:G:GG	acceptor_gain	1.0000
1:100137018:GCACA:G	acceptor_gain	1.0000
1:100137086:G:GG	donor_gain	1.0000
1:100139642:T:TA	acceptor_gain	1.0000
1:100139646:A:AG	acceptor_gain	1.0000
1:100139646:AAG:A	acceptor_gain	1.0000
1:100139646:AAGG:A	acceptor_loss	1.0000
1:100139647:A:G	acceptor_gain	1.0000
1:100139647:AGG:A	acceptor_loss	1.0000
1:100139648:G:A	acceptor_gain	1.0000
1:100139707:AATTA:A	donor_gain	1.0000
1:100139708:ATTA:A	donor_gain	1.0000
1:100139708:ATTAG:A	donor_loss	1.0000
1:100139709:TTA:T	donor_gain	1.0000
1:100139710:TA:T	donor_gain	1.0000

AlphaMissense

3165 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:100136909:T:C	C59R	0.999
1:100137059:T:A	C79S	0.999
1:100137059:T:C	C79R	0.999
1:100137060:G:C	C79S	0.999
1:100136909:T:A	C59S	0.998
1:100136910:G:C	C59S	0.998
1:100137024:T:A	V67E	0.998
1:100137047:C:G	H75D	0.998
1:100137049:T:A	H75Q	0.998
1:100137049:T:G	H75Q	0.998
1:100140910:T:A	V187D	0.998
1:100140997:A:T	E216V	0.998
1:100133256:T:A	C30S	0.997
1:100133256:T:C	C30R	0.997
1:100133257:G:C	C30S	0.997
1:100133289:T:C	C41R	0.997
1:100136902:A:C	R56S	0.997
1:100136902:A:T	R56S	0.997
1:100136927:C:G	H65D	0.997
1:100137019:C:A	H65Q	0.997
1:100137019:C:G	H65Q	0.997
1:100137060:G:T	C79F	0.997
1:100140852:G:C	A168P	0.997
1:100141019:G:C	K223N	0.997
1:100141019:G:T	K223N	0.997
1:100144121:G:C	K265N	0.997
1:100144121:G:T	K265N	0.997
1:100133223:T:A	C19S	0.996
1:100133224:G:C	C19S	0.996
1:100133257:G:A	C30Y	0.996

dbSNP variants (sampled 300 via entrez): RS1000091392 (1:100150171 A>G), RS1000179209 (1:100139129 G>A), RS1000278459 (1:100133107 G>A,C), RS1000491855 (1:100138485 A>T), RS1000523331 (1:100149219 T>C), RS1000600505 (1:100134133 A>C), RS1000805184 (1:100140307 G>A), RS1000965989 (1:100142569 G>A), RS1001234920 (1:100143538 C>G,T), RS1001554546 (1:100135724 T>C), RS1001814691 (1:100150457 A>C), RS1002753849 (1:100136167 A>G), RS1003106960 (1:100133022 G>A), RS1003227083 (1:100150301 T>C), RS1003349806 (1:100137548 T>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

0 associations (top):

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	decreases expression, decreases methylation, increases expression	3
GSK-J4	decreases expression	1
methylmercuric chloride	decreases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	decreases methylation	1
deoxynivalenol	increases expression	1
testosterone undecanoate	affects cotreatment, decreases expression	1
CGP 52608	affects binding, increases reaction	1
2-palmitoylglycerol	increases expression	1
abrine	increases expression	1
jinfukang	affects cotreatment, decreases expression	1
Irinotecan	decreases expression	1
Sunitinib	decreases expression	1
Fulvestrant	increases methylation	1
Acetaminophen	decreases expression	1
Air Pollutants	decreases expression, increases abundance	1
Cannabidiol	decreases expression	1
Cisplatin	affects cotreatment, decreases expression	1
Estradiol	increases expression	1
Gold	decreases expression	1
Haloperidol	decreases expression	1
Dronabinol	increases expression	1
Theophylline	increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Tretinoin	decreases expression	1
Urethane	decreases expression	1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	decreases expression	1
Cyclosporine	decreases expression	1
Aflatoxin B1	increases methylation	1
Levonorgestrel	affects cotreatment, decreases expression	1

Clinical trials (associated diseases)

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