TRPT1

Summary

TRPT1 (tRNA phosphotransferase 1, HGNC:20316) is a protein-coding gene on chromosome 11q13.1, encoding tRNA 2’-phosphotransferase 1 (Q86TN4). Catalyzes the last step of tRNA splicing, the transfer of the splice junction 2’-phosphate from ligated tRNA to NAD to produce ADP-ribose 1’’-2’’ cyclic phosphate.

Predicted to enable tRNA 2’-phosphotransferase activity. Predicted to be involved in tRNA splicing, via endonucleolytic cleavage and ligation. Predicted to act upstream of or within regulation of protein kinase activity.

Source: NCBI Gene 83707 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 57 total
• MANE Select transcript: NM_001033678

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:20316
Approved symbol	TRPT1
Name	tRNA phosphotransferase 1
Location	11q13.1
Locus type	gene with protein product
Status	Approved
Aliases	MGC11134
Ensembl gene	ENSG00000149743
Ensembl biotype	protein_coding
OMIM	610470
Entrez	83707

Gene structure

Transcript identifiers

Ensembl transcripts: 41 — 33 protein_coding, 7 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000317459, ENST00000394546, ENST00000394547, ENST00000536158, ENST00000536234, ENST00000537907, ENST00000539436, ENST00000539595, ENST00000540472, ENST00000541278, ENST00000541928, ENST00000542040, ENST00000544286, ENST00000545812, ENST00000546089, ENST00000546133, ENST00000877499, ENST00000877500, ENST00000877501, ENST00000877502, ENST00000877503, ENST00000877504, ENST00000877505, ENST00000877506, ENST00000877507, ENST00000935365, ENST00000935366, ENST00000935367, ENST00000935368, ENST00000935369, ENST00000935370, ENST00000935371, ENST00000935372, ENST00000935373, ENST00000962780, ENST00000962781, ENST00000962782, ENST00000962783, ENST00000962784, ENST00000962785, ENST00000962786

RefSeq mRNA: 7 — MANE Select: NM_001033678 NM_001033678, NM_001160389, NM_001160390, NM_001160392, NM_001160393, NM_001330298, NM_031472

CCDS: CCDS31595, CCDS44639, CCDS53652, CCDS53653, CCDS81579

Canonical transcript exons

ENST00000317459 — 8 exons

Exon	Start	End
ENSE00000992267	64224543	64224717
ENSE00000992268	64224285	64224341
ENSE00001196076	64223816	64223967
ENSE00001297860	64226050	64226186
ENSE00003547097	64225786	64225869
ENSE00003547744	64225499	64225580
ENSE00003637626	64224100	64224210
ENSE00003686043	64224801	64224970

Expression profiles

Bgee: expression breadth ubiquitous, 248 present calls, max score 97.56.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 17.0907 / max 96.4669, expressed in 1787 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
120354	16.4012	1786
120355	0.6895	442

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
gastrocnemius	UBERON:0001388	97.56	gold quality
left ventricle myocardium	UBERON:0006566	97.51	gold quality
muscle of leg	UBERON:0001383	97.20	gold quality
apex of heart	UBERON:0002098	96.95	gold quality
hindlimb stylopod muscle	UBERON:0004252	96.83	gold quality
mucosa of transverse colon	UBERON:0004991	96.07	gold quality
heart left ventricle	UBERON:0002084	96.01	gold quality
metanephros cortex	UBERON:0010533	95.99	gold quality
tibialis anterior	UBERON:0001385	95.92	silver quality
cardiac ventricle	UBERON:0002082	95.85	gold quality
cardiac muscle of right atrium	UBERON:0003379	95.71	gold quality
right atrium auricular region	UBERON:0006631	95.44	gold quality
cardiac atrium	UBERON:0002081	95.33	gold quality
quadriceps femoris	UBERON:0001377	95.19	gold quality
body of pancreas	UBERON:0001150	95.13	gold quality
vastus lateralis	UBERON:0001379	94.92	gold quality
heart	UBERON:0000948	94.90	gold quality
lower esophagus mucosa	UBERON:0035834	94.80	gold quality
right lobe of thyroid gland	UBERON:0001119	94.75	gold quality
adenohypophysis	UBERON:0002196	94.56	gold quality
body of stomach	UBERON:0001161	94.46	gold quality
skeletal muscle tissue	UBERON:0001134	94.44	gold quality
cortex of kidney	UBERON:0001225	94.42	gold quality
transverse colon	UBERON:0001157	94.30	gold quality
left testis	UBERON:0004533	94.24	gold quality
right adrenal gland	UBERON:0001233	94.19	gold quality
right testis	UBERON:0004534	94.17	gold quality
left lobe of thyroid gland	UBERON:0001120	94.15	gold quality
right adrenal gland cortex	UBERON:0035827	94.11	gold quality
muscle tissue	UBERON:0002385	94.05	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	11.36
E-CURD-10	no	133.75
E-MTAB-10290	no	61.38

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 2)

• ADP-ribosylation of RNA in mammalian cells is mediated by TRPT1 and multiple PARPs. (PMID:36018800)
• Structural and biochemical insights into the molecular mechanism of TRPT1 for nucleic acid ADP-ribosylation. (PMID:37334830)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	trpt1	ENSDARG00000037628
mus_musculus	Trpt1	ENSMUSG00000047656
rattus_norvegicus	Trpt1	ENSRNOG00000023023
drosophila_melanogaster	Tpt	FBGN0053057

Protein

Protein identifiers

tRNA 2’-phosphotransferase 1 — Q86TN4 (reviewed: Q86TN4)

All UniProt accessions (5): Q86TN4, F5H1K3, F5H6B6, F5H8A0, H0YGY9

UniProt curated annotations — full annotation on UniProt →

Function. Catalyzes the last step of tRNA splicing, the transfer of the splice junction 2’-phosphate from ligated tRNA to NAD to produce ADP-ribose 1’’-2’’ cyclic phosphate.

Tissue specificity. Widely expressed. Weakly or not expressed in lung, spleen, small intestine and peripheral blood leukocytes.

Similarity. Belongs to the KptA/TPT1 family.

Isoforms (4)

UniProt ID	Names	Canonical?
Q86TN4-1	1	yes
Q86TN4-2	2
Q86TN4-3	3
Q86TN4-4	4

RefSeq proteins (7): NP_001028850, NP_001153861, NP_001153862, NP_001153864, NP_001153865, NP_001317227, NP_113660 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002745	Ptrans_KptA/Tpt1	Family
IPR042080	RNA_2’-PTrans_N	Homologous_superfamily
IPR042081	RNA_2’-PTrans_C	Homologous_superfamily

Pfam: PF01885

Enzyme classification (BRENDA):

• EC 2.7.1.160 — 2’-phosphotransferase (BRENDA: 40 organisms, 34 substrates, 16 inhibitors, 17 Km, 17 kcat entries)

Substrate kinetics (BRENDA)

4 substrates with measured Km, best-characterized 4. Km ranges are aggregated across organisms/conditions.

Substrate	Km (mM)	Measurements
3-MER 2’ PHOSPHORYLATED RNA	0.0001–0.04	10
18-MER 2’ PHOSPHORYLATED RNA	—	2
2’-PHOSPHO-[LIGATED TRNA]	—	2
8-MER 2’ PHOSPHORYLATED RNA	—	2

Catalyzed reactions (Rhea), 1 shown:

• 2’-phospho-[ligated tRNA] + NAD(+) = mature tRNA + ADP-alpha-D-ribose 1’’,2’’-cyclic phosphate + nicotinamide (RHEA:23324)

UniProt features (34 total): strand 11, helix 7, turn 4, sequence variant 3, splice variant 3, region of interest 2, modified residue 2, chain 1, compositionally biased region 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
7YW3	X-RAY DIFFRACTION	2.5

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q86TN4-F1	85.75	0.72

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 (2): 1, 240

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 68 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_COLON_TUMORAL_MACROPHAGE_DN, GOBP_TRNA_METABOLIC_PROCESS, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, chr11q13, CAGCTG_AP4_Q5, GOBP_RNA_SPLICING_VIA_ENDONUCLEOLYTIC_CLEAVAGE_AND_LIGATION, HNF4_DR1_Q3, GOBP_RNA_SPLICING, PPAR_DR1_Q2, NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_DN, ELK1_01, GOBP_TRNA_PROCESSING, NUYTTEN_EZH2_TARGETS_DN, SCGGAAGY_ELK1_02, GOMF_TRANSFERASE_ACTIVITY_TRANSFERRING_PHOSPHORUS_CONTAINING_GROUPS

GO Biological Process (2): tRNA splicing, via endonucleolytic cleavage and ligation (GO:0006388), tRNA processing (GO:0008033)

GO Molecular Function (3): tRNA 2’-phosphotransferase activity (GO:0000215), protein binding (GO:0005515), transferase activity (GO:0016740)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
RNA splicing, via endonucleolytic cleavage and ligation	1
tRNA processing	1
RNA processing	1
tRNA metabolic process	1
phosphotransferase activity, alcohol group as acceptor	1
catalytic activity, acting on a tRNA	1
binding	1
catalytic activity	1

Protein interactions and networks

STRING

750 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TRPT1	PARP10	Q53GL7	732
TRPT1	PARP11	Q9NR21	687
TRPT1	PARP15	Q460N3	673
TRPT1	ADPRS	Q9NX46	619
TRPT1	PARP3	Q9Y6F1	616
TRPT1	RTCA	O00442	605
TRPT1	RTCB	Q9Y3I0	604
TRPT1	TSEN34	Q9BSV6	595
TRPT1	TSEN2	Q8NCE0	559
TRPT1	MACROD1	Q9BQ69	546
TRPT1	ZC3HAV1	Q7Z2W4	543
TRPT1	NUDT22	Q9BRQ3	532
TRPT1	TSEN54	Q7Z6J9	529
TRPT1	PUSL1	Q8N0Z8	507
TRPT1	ISY1	Q9ULR0	501

IntAct

10 interactions, top by confidence:

A	B	Type	Score
TRPT1	GAPDHS	psi-mi:“MI:0915”(physical association)	0.400
TRAF2	TRPT1	psi-mi:“MI:0915”(physical association)	0.370
LIN28A	MEX3A	psi-mi:“MI:0914”(association)	0.350
TEX19	ZNF316	psi-mi:“MI:0914”(association)	0.350
TRPT1	STRIP1	psi-mi:“MI:0914”(association)	0.350
TEX19	FYN	psi-mi:“MI:0914”(association)	0.350
CEBPA	MYO1C	psi-mi:“MI:0914”(association)	0.350
ERBB2	DNM1L	psi-mi:“MI:0914”(association)	0.350
MYC	AP3B1	psi-mi:“MI:0914”(association)	0.350

BioGRID (27): TRPT1 (Two-hybrid), DYNC1LI1 (Affinity Capture-MS), STRIP1 (Affinity Capture-MS), ZYG11B (Affinity Capture-MS), TRPT1 (Two-hybrid), TRPT1 (Two-hybrid), TRPT1 (Negative Genetic), TRPT1 (Affinity Capture-RNA), DYNC1LI1 (Affinity Capture-MS), TRPT1 (Affinity Capture-MS), SERPINA10 (Affinity Capture-MS), STRIP1 (Affinity Capture-MS), ZYG11B (Affinity Capture-MS), GAPDHS (Affinity Capture-MS), TRPT1 (Affinity Capture-MS)

ESM2 similar proteins: A4GXA9, A7E3N7, A8MXQ7, A8VU90, F1MH07, F1MLB4, F1MX48, O70348, O77932, P58107, Q0V8J4, Q0VCI6, Q3ULW8, Q3ZBM7, Q4KM32, Q4V7F5, Q561R2, Q56A04, Q58CQ5, Q5EAR5, Q5HZH2, Q643R3, Q66H85, Q6MG77, Q6NVG1, Q6PAT0, Q7T0L4, Q80UU1, Q80XL1, Q86TN4, Q8CJ00, Q8K3A2, Q8N9W5, Q8NFF5, Q8TDZ2, Q8VDP3, Q91ZJ0, Q924T7, Q95K25, Q96EP0

Diamond homologs: A2BMI7, A3DJX6, A5FLZ4, A6UXB5, A7ZVN0, A8A858, A9B356, B0C090, B1LDT4, B1VP90, B2IZ22, B2TYV0, B5ZQT5, B6I2L3, B6YXF3, B7LDY6, B7LXP0, B7MMM2, B7NGY8, B9JFP7, C4ZT19, C6DJM6, O28719, O29841, O57899, P39380, Q02V26, Q037J6, Q0SWM0, Q0T8X6, Q0TUT1, Q1MG28, Q2SQM5, Q395F2, Q3M450, Q3ZBM7, Q46DV8, Q48DQ3, Q4K4C7, Q5JFX3

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	37
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1736 predictions. Top by Δscore:

Variant	Effect	Δscore
11:64224098:A:AC	donor_gain	1.0000
11:64224099:C:CC	donor_gain	1.0000
11:64224599:C:A	donor_gain	1.0000
11:64224878:T:TA	donor_gain	1.0000
11:64224112:G:C	donor_gain	0.9900
11:64224542:CCA:C	donor_gain	0.9900
11:64224594:T:TA	donor_gain	0.9900
11:64224814:C:CA	donor_gain	0.9900
11:64224857:G:C	donor_gain	0.9900
11:64225498:CCAG:C	donor_gain	0.9900
11:64226005:C:A	donor_gain	0.9900
11:64226028:AGGC:A	donor_gain	0.9900
11:64224123:T:TA	donor_gain	0.9800
11:64224280:CTCA:C	donor_loss	0.9800
11:64224281:TCA:T	donor_loss	0.9800
11:64224282:CA:C	donor_loss	0.9800
11:64224284:C:CT	donor_loss	0.9800
11:64224715:TACC:T	acceptor_loss	0.9800
11:64224718:CTG:C	acceptor_loss	0.9800
11:64225493:ACTT:A	donor_loss	0.9800
11:64225494:CTTA:C	donor_loss	0.9800
11:64225495:TTA:T	donor_loss	0.9800
11:64225496:TACC:T	donor_loss	0.9800
11:64225497:A:AC	donor_gain	0.9800
11:64225497:A:T	donor_loss	0.9800
11:64225498:C:CC	donor_gain	0.9800
11:64225498:C:CT	donor_loss	0.9800
11:64225578:GTCC:G	acceptor_loss	0.9800
11:64225581:CTGA:C	acceptor_loss	0.9800
11:64225993:C:CT	donor_gain	0.9800

AlphaMissense

1625 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:64224867:G:C	F87L	0.972
11:64224867:G:T	F87L	0.972
11:64224869:A:G	F87L	0.972
11:64224963:G:C	F55L	0.966
11:64224963:G:T	F55L	0.966
11:64224965:A:G	F55L	0.966
11:64224829:A:T	I100N	0.959
11:64224826:C:G	R101P	0.955
11:64224585:G:C	H154D	0.950
11:64224829:A:G	I100T	0.950
11:64225538:G:T	R40S	0.946
11:64224314:A:T	V177E	0.941
11:64224868:A:G	F87S	0.931
11:64224293:G:T	A184D	0.930
11:64224595:C:A	R150S	0.927
11:64224595:C:G	R150S	0.927
11:64224308:A:T	I179N	0.925
11:64224868:A:C	F87C	0.924
11:64224810:A:C	H106Q	0.922
11:64224810:A:T	H106Q	0.922
11:64224197:G:C	F191L	0.921
11:64224197:G:T	F191L	0.921
11:64224199:A:G	F191L	0.921
11:64225535:G:C	H41D	0.918
11:64224829:A:C	I100S	0.916
11:64224876:C:A	K84N	0.916
11:64224876:C:G	K84N	0.916
11:64224659:A:T	V129D	0.915
11:64224927:G:C	F67L	0.914
11:64224927:G:T	F67L	0.914

dbSNP variants (sampled 300 via entrez): RS1000445974 (11:64226339 G>A), RS1000774539 (11:64226560 A>C,G), RS1002898986 (11:64224472 T>G), RS1003789548 (11:64223513 C>A,T), RS1004128134 (11:64227785 G>A), RS1006219039 (11:64225139 A>G), RS1006610882 (11:64225980 C>A,T), RS1006699881 (11:64224982 C>A,T), RS1007116205 (11:64223776 A>C,G), RS1007142168 (11:64224733 G>A), RS1007468731 (11:64225205 T>C,G), RS1007828789 (11:64225424 C>G,T), RS1009092108 (11:64226598 C>G,T), RS1009555978 (11:64226383 G>A,T), RS1010457976 (11:64224414 G>A)

Disease associations

OMIM: gene MIM:610470 | 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
GCST001154_5	Attention deficit hyperactivity disorder	4.000000e-06
GCST001725_12	Inflammatory bowel disease	4.000000e-11
GCST004132_98	Crohn’s disease	5.000000e-06
GCST010136_47	Fruit consumption	9.000000e-10

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

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression, affects expression, increases methylation	3
sodium arsenite	affects cotreatment, increases abundance, increases expression, decreases expression	2
methacrylaldehyde	affects cotreatment, increases expression, increases abundance	2
Acrolein	affects cotreatment, increases expression, increases abundance	2
Arsenic	increases abundance, increases expression, decreases expression, affects cotreatment	2
Ozone	affects cotreatment, increases expression, increases abundance	2
aristolochic acid I	decreases expression	1
FR900359	increases phosphorylation	1
triphenyl phosphate	affects expression	1
alpha-pinene	affects cotreatment, increases expression, increases abundance	1
beta-lapachone	decreases expression	1
manganese chloride	increases expression, affects cotreatment, increases abundance	1
benzo(e)pyrene	increases methylation	1
coumarin	increases phosphorylation	1
di-n-butylphosphoric acid	affects expression	1
perfluorooctane sulfonic acid	increases expression	1
jinfukang	affects cotreatment, increases expression	1
Air Pollutants	affects cotreatment, increases abundance, increases expression	1
Cisplatin	affects cotreatment, increases expression	1
Gasoline	affects cotreatment, decreases expression, increases abundance	1
Hydralazine	affects cotreatment, increases expression	1
Ivermectin	decreases expression	1
Manganese	affects cotreatment, increases abundance, increases expression	1
Methapyrilene	increases methylation	1
Polycyclic Aromatic Hydrocarbons	increases abundance, affects cotreatment, decreases expression	1
Smoke	decreases expression	1
Thiram	decreases expression	1
Urethane	decreases expression	1
Cadmium Chloride	increases expression	1
Okadaic Acid	decreases expression	1

Clinical trials (associated diseases)

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