TRMT2A

Summary

TRMT2A (tRNA methyltransferase 2A, HGNC:24974) is a protein-coding gene on chromosome 22q11.21, encoding tRNA (uracil-5-)-methyltransferase homolog A (Q8IZ69). S-adenosyl-L-methionine-dependent methyltransferase that catalyzes the formation of 5-methyl-uridine in tRNAs and some mRNAs.

The protein encoded by this gene is of unknown function. However, it is orthologous to the mouse Trmt2a gene and contains an RNA methyltransferase domain. Expression of this gene varies during the cell cycle, with aberrant expression being a possible biomarker in certain breast cancers. Several transcript variants encoding two different isoforms have been found for this gene.

Source: NCBI Gene 27037 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 112 total — 3 pathogenic, 1 likely-pathogenic
• MANE Select transcript: NM_022727

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24974
Approved symbol	TRMT2A
Name	tRNA methyltransferase 2A
Location	22q11.21
Locus type	gene with protein product
Status	Approved
Aliases	HTF9C
Ensembl gene	ENSG00000099899
Ensembl biotype	protein_coding
OMIM	611151
Entrez	27037

Gene structure

Transcript identifiers

Ensembl transcripts: 27 — 16 protein_coding, 9 retained_intron, 1 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000252136, ENST00000403707, ENST00000404751, ENST00000439169, ENST00000444256, ENST00000444845, ENST00000445045, ENST00000459644, ENST00000463710, ENST00000464535, ENST00000480339, ENST00000480460, ENST00000487378, ENST00000487668, ENST00000488335, ENST00000492988, ENST00000494641, ENST00000494820, ENST00000856769, ENST00000914134, ENST00000949380, ENST00000949381, ENST00000949382, ENST00000949383, ENST00000949384, ENST00000949385, ENST00000949386

RefSeq mRNA: 4 — MANE Select: NM_022727 NM_001257994, NM_001331039, NM_022727, NM_182984

CCDS: CCDS13774, CCDS58793, CCDS82693

Canonical transcript exons

ENST00000252136 — 12 exons

Exon	Start	End
ENSE00001191993	20111875	20112794
ENSE00001873673	20116883	20117226
ENSE00003481680	20114761	20114876
ENSE00003490094	20114574	20114685
ENSE00003527953	20113432	20113507
ENSE00003531490	20115672	20115780
ENSE00003546813	20112911	20113007
ENSE00003597523	20113686	20113808
ENSE00003622657	20114965	20115079
ENSE00003628675	20113118	20113234
ENSE00003681824	20115266	20115447
ENSE00003689279	20116038	20116612

Expression profiles

Bgee: expression breadth ubiquitous, 206 present calls, max score 96.63.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 26.6742 / max 302.4231, expressed in 1813 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
193183	21.7738	1812
193182	4.1725	1593
209393	0.7279	129

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
granulocyte	CL:0000094	96.63	gold quality
right uterine tube	UBERON:0001302	96.56	gold quality
adenohypophysis	UBERON:0002196	96.21	gold quality
left testis	UBERON:0004533	96.06	gold quality
right hemisphere of cerebellum	UBERON:0014890	95.95	gold quality
right testis	UBERON:0004534	95.90	gold quality
right lobe of thyroid gland	UBERON:0001119	95.83	gold quality
right lobe of liver	UBERON:0001114	95.70	gold quality
body of pancreas	UBERON:0001150	95.37	gold quality
apex of heart	UBERON:0002098	95.36	gold quality
cerebellar hemisphere	UBERON:0002245	95.32	gold quality
left adrenal gland cortex	UBERON:0035825	95.22	gold quality
cerebellar cortex	UBERON:0002129	95.20	gold quality
right adrenal gland cortex	UBERON:0035827	95.20	gold quality
right adrenal gland	UBERON:0001233	95.18	gold quality
left lobe of thyroid gland	UBERON:0001120	95.17	gold quality
left adrenal gland	UBERON:0001234	95.02	gold quality
body of stomach	UBERON:0001161	94.96	gold quality
left uterine tube	UBERON:0001303	94.82	gold quality
right ovary	UBERON:0002118	94.82	gold quality
spleen	UBERON:0002106	94.72	gold quality
endocervix	UBERON:0000458	94.68	gold quality
body of uterus	UBERON:0009853	94.63	gold quality
minor salivary gland	UBERON:0001830	94.60	gold quality
nerve	UBERON:0001021	94.56	gold quality
tibial nerve	UBERON:0001323	94.56	gold quality
left ovary	UBERON:0002119	94.48	gold quality
lower esophagus mucosa	UBERON:0035834	94.48	gold quality
metanephros cortex	UBERON:0010533	94.47	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	94.39	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	2.95

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

14 targeting TRMT2A, 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-12119	99.87	68.35	1653
HSA-MIR-6887-3P	99.66	67.83	1778
HSA-MIR-7515	99.31	68.22	1795
HSA-MIR-361-3P	99.19	66.45	1381
HSA-MIR-6852-5P	99.17	66.69	2073
HSA-MIR-6791-5P	99.16	65.92	1844
HSA-MIR-4292	99.16	65.57	1767
HSA-MIR-511-5P	98.97	70.94	2268
HSA-MIR-3190-5P	98.87	64.89	1345
HSA-MIR-1227-5P	98.65	65.32	1549
HSA-MIR-6804-5P	98.39	65.77	1084
HSA-MIR-4800-5P	97.22	65.91	324
HSA-MIR-1291	96.28	65.89	1224
HSA-MIR-6775-3P	95.76	65.91	982

Literature-anchored findings (GeneRIF, showing 6)

• Single nucleotid polymorphisms of this gene may be associated with a deficit in sustained attention within schizophrenia, in a Taiwanese cohort. (PMID:18075473)
• TRMT2A staining showed a strong correlation with likelihood of recurrence at five years in 67 HER2+ breast cancer. (PMID:20307320)
• tRNA methyltransferase 2 homolog A (TRMT2A) protein harbors an RNA recognition motif in the N-terminus and the conserved uracil-C5-methyltransferase domain of the TrmA family in the C-terminus. TRMT2A predominantly localizes to the nucleus in HeLa cells. TRMT2A-overexpressing cells display decreased cell proliferation and altered DNA content, while TRMT2A-deficient cells exhibit increased growth. (PMID:30502085)
• Our associated finding of extensive irreversible TRMT2A-tRNA crosslinking in vivo following 5-Fluorouracil exposure is also intriguing, as it suggests a tangible mechanism for a previously suspected RNA-dependent route of Fluorouracil-mediated cytotoxicity. (PMID:31361898)
• m(5)U54 tRNA Hypomodification by Lack of TRMT2A Drives the Generation of tRNA-Derived Small RNAs. (PMID:33799331)
• Human TRMT2A methylates tRNA and contributes to translation fidelity. (PMID:37395448)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	trmt2a	ENSDARG00000002830
mus_musculus	Trmt2a	ENSMUSG00000022721
rattus_norvegicus	Trmt2a	ENSRNOG00000001885
drosophila_melanogaster	CG3808	FBGN0036838
caenorhabditis_elegans		WBGENE00019241

Paralogs (1): TRMT2B (ENSG00000188917)

Protein

Protein identifiers

tRNA (uracil-5-)-methyltransferase homolog A — Q8IZ69 (reviewed: Q8IZ69)

Alternative names: mRNA (uracil-5-)-methyltransferase TRMT2A

All UniProt accessions (6): Q8IZ69, A0A994J4Q5, C9K041, F2Z2W7, H7BZZ4, H7C100

UniProt curated annotations — full annotation on UniProt →

Function. S-adenosyl-L-methionine-dependent methyltransferase that catalyzes the formation of 5-methyl-uridine in tRNAs and some mRNAs. Mainly catalyzes the methylation of uridine at position 54 (m5U54) in cytosolic tRNAs. Also able to mediate the formation of 5-methyl-uridine in some mRNAs.

Subcellular location. Cytoplasm. Cytosol.

Similarity. Belongs to the class I-like SAM-binding methyltransferase superfamily. RNA M5U methyltransferase family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q8IZ69-1	1	yes
Q8IZ69-2	2

RefSeq proteins (4): NP_001244923, NP_001317968, NP_073564, NP_892029 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000504	RRM_dom	Domain
IPR010280	U5_MeTrfase_fam	Family
IPR012677	Nucleotide-bd_a/b_plait_sf	Homologous_superfamily
IPR029063	SAM-dependent_MTases_sf	Homologous_superfamily
IPR034262	TRMT2A_RRM	Domain
IPR035979	RBD_domain_sf	Homologous_superfamily
IPR045850	TRM2_met	Family

Pfam: PF05958

Enzyme classification (BRENDA):

• EC 2.1.1.35 — tRNA (uracil54-C5)-methyltransferase (BRENDA: 10 organisms, 132 substrates, 40 inhibitors, 24 Km, 7 kcat entries)

Substrate kinetics (BRENDA)

16 substrates with measured Km, best-characterized 15. Km ranges are aggregated across organisms/conditions.

Substrate	Km (mM)	Measurements
S-ADENOSYL-L-METHIONINE	0.002–0.018	5
URACIL54 IN 11MER OF THE T-ARM OF E. COLI TRNA1-	0.0037–0.004	2
URACIL54 IN YEAST TRNA-PHE	0.0004–0.0008	2
DNA ANALOG OF THE T-STEM/LOOP DOMAIN OF YEAST TR	0.0145	1
METHYL DEFICIENT TRNA	0.025	1
URACIL IN ASH1 E3 MRNA	0.0008	1
URACIL54 IN 17MER OF THE T-ARM OF E. COLI TRNA1-	0.005	1
URACIL54 IN METHYL DEFICIENT TRNA FROM E. COLI	0.29	1
URACIL54 IN TRNAGLN	0.0015	1
URACIL54 IN TRNAPHE	0.0007	1
URACIL54 IN UNMODIFIED E. COLI TRNA1-VAL	0.0028	1
URACIL54 IN UNMODIFIED T-STEM/LOOP DOMAIN OF YEA	0.0057	1
URACIL54 IN UNMODIFIED YEAST TRNA-PHE TPSIC-STEM	0.0156	1
URACIL54 IN WHEAT GERM TRNA1-GLY	0.0011	1
URACIL54 IN YEAST TRNA1-PHE	0.0008	1

Catalyzed reactions (Rhea), 2 shown:

• uridine(54) in tRNA + S-adenosyl-L-methionine = 5-methyluridine(54) in tRNA + S-adenosyl-L-homocysteine + H(+) (RHEA:42712)
• a uridine in mRNA + S-adenosyl-L-methionine = a 5-methyluridine in mRNA + S-adenosyl-L-homocysteine + H(+) (RHEA:69863)

UniProt features (28 total): strand 4, binding site 3, region of interest 3, compositionally biased region 3, active site 2, modified residue 2, splice variant 2, sequence variant 2, helix 2, chain 1, domain 1, sequence conflict 1, turn 1, coiled-coil region 1

Structure

Experimental structures (PDB)

2 structures.

PDB	Method	Resolution (Å)
7NTO	X-RAY DIFFRACTION	1.23
7NTN	X-RAY DIFFRACTION	2.02

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8IZ69-F1	82.47	0.59

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (2): 581 (proton acceptor); 538 (nucleophile)

Ligand- & substrate-binding residues (3): 411; 461; 510

Post-translational modifications (2): 378, 602

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 163 (showing top): RNGTGGGC_UNKNOWN, E2F_Q4, E2F_Q4_01, PAX4_01, E2F4DP1_01, GAANYNYGACNY_UNKNOWN, CMYB_01, STARK_PREFRONTAL_CORTEX_22Q11_DELETION_DN, GOBP_TRNA_METABOLIC_PROCESS, TGACCTY_ERR1_Q2, E2F1DP1_01, E2F_Q3, E2F1DP2_01, MYCMAX_01, HESS_TARGETS_OF_HOXA9_AND_MEIS1_UP

GO Biological Process (4): mRNA processing (GO:0006397), tRNA processing (GO:0008033), methylation (GO:0032259), RNA processing (GO:0006396)

GO Molecular Function (8): RNA binding (GO:0003723), C-methyltransferase activity (GO:0008169), tRNA (uracil(54)-C5)-methyltransferase activity, S-adenosyl methionine-dependent (GO:0030697), nucleic acid binding (GO:0003676), protein binding (GO:0005515), methyltransferase activity (GO:0008168), RNA methyltransferase activity (GO:0008173), transferase activity (GO:0016740)

GO Cellular Component (2): cytosol (GO:0005829), cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
RNA processing	2
methyltransferase activity	2
binding	2
cellular anatomical structure	2
mRNA metabolic process	1
tRNA metabolic process	1
metabolic process	1
gene expression	1
RNA biosynthetic process	1
primary metabolic process	1
nucleic acid binding	1
S-adenosylmethionine-dependent methyltransferase activity	1
tRNA (uridine) methyltransferase activity	1
transferase activity, transferring one-carbon groups	1
catalytic activity, acting on RNA	1
catalytic activity	1
cytoplasm	1
intracellular anatomical structure	1

Protein interactions and networks

STRING

2124 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TRMT2A	RANBP1	P43487	929
TRMT2A	NDRG1	Q92597	663
TRMT2A	SLC7A5	Q01650	643
TRMT2A	TANGO2	Q6ICL3	622
TRMT2A	GNB1L	Q9BYB4	609
TRMT2A	ZDHHC8	Q9ULC8	607
TRMT2A	DGCR2	P98153	598
TRMT2A	CEACAM5	P06731	593
TRMT2A	SDR39U1	Q9NRG7	577
TRMT2A	RAN	P17080	549
TRMT2A	MRPL40	Q9NQ50	535
TRMT2A	ARVCF	O00192	533
TRMT2A	TYW2	Q53H54	526
TRMT2A	UFD1	Q92890	519
TRMT2A	NSUN2	Q08J23	518

IntAct

120 interactions, top by confidence:

A	B	Type	Score
ANKRD44	ANKRD28	psi-mi:“MI:0914”(association)	0.710
TRMT2A	APPBP2	psi-mi:“MI:0915”(physical association)	0.560
TRMT2A	ZNF837	psi-mi:“MI:0915”(physical association)	0.560
TRMT2A	PICK1	psi-mi:“MI:0915”(physical association)	0.560
MCC	TRMT2A	psi-mi:“MI:0915”(physical association)	0.560
TLE5	TRMT2A	psi-mi:“MI:0915”(physical association)	0.560
MESD	TRMT2A	psi-mi:“MI:0915”(physical association)	0.560
MEOX2	TRMT2A	psi-mi:“MI:0915”(physical association)	0.560
UPK3B	AP1G2	psi-mi:“MI:0914”(association)	0.560
FAM174A	BLTP3B	psi-mi:“MI:0914”(association)	0.530
CLEC11A	VWA8	psi-mi:“MI:0914”(association)	0.530
LAMP3	METTL15	psi-mi:“MI:0914”(association)	0.530
ZNRD2	MYO9A	psi-mi:“MI:0914”(association)	0.530
CREB3	MYO9A	psi-mi:“MI:0914”(association)	0.530
VASP	GTPBP1	psi-mi:“MI:0914”(association)	0.530
PNMA2	CCDC85C	psi-mi:“MI:0914”(association)	0.530
S100A4	OIP5	psi-mi:“MI:0914”(association)	0.530
ZNRD2	CCDC85C	psi-mi:“MI:0914”(association)	0.530
IRF7	AIP	psi-mi:“MI:0914”(association)	0.500
TRMT2A	CDCA2	psi-mi:“MI:0915”(physical association)	0.400
TRMT2A	ANXA7	psi-mi:“MI:0915”(physical association)	0.370
ATP1B1	TRMT2A	psi-mi:“MI:0915”(physical association)	0.370
TRMT2A	CDK4	psi-mi:“MI:0915”(physical association)	0.370
TRMT2A	CDKN1A	psi-mi:“MI:0915”(physical association)	0.370
GADD45G	TRMT2A	psi-mi:“MI:0915”(physical association)	0.370
TRMT2A	AIMP2	psi-mi:“MI:0915”(physical association)	0.370
TRMT2A	PIK3R3	psi-mi:“MI:0915”(physical association)	0.370
TRMT2A	PIN1	psi-mi:“MI:0915”(physical association)	0.370
RASA1	TRMT2A	psi-mi:“MI:0915”(physical association)	0.370
TRMT2A	RCC1	psi-mi:“MI:0915”(physical association)	0.370

BioGRID (176): TRMT2A (Affinity Capture-RNA), TRMT2A (Affinity Capture-MS), TRMT2A (Affinity Capture-MS), SMYD3 (Co-fractionation), TRMT2A (Co-fractionation), TRMT2A (Reconstituted Complex), TRMT2A (Affinity Capture-MS), TRMT2A (Affinity Capture-MS), TRMT2A (Affinity Capture-MS), TRMT2A (Affinity Capture-MS), TRMT2A (Affinity Capture-MS), SMARCAD1 (Affinity Capture-MS), ANKRD44 (Affinity Capture-MS), PBK (Affinity Capture-MS), PPP6R2 (Affinity Capture-MS)

ESM2 similar proteins: A0A0B4J1F4, A0A0G2JXN2, A2AWP8, A2RRH5, C9J798, O43374, O70277, O95294, P04629, P59926, Q0GA42, Q13368, Q14318, Q16512, Q29RM4, Q2HY40, Q2T9P3, Q2TBA3, Q5BIM1, Q5M7W1, Q5R5M3, Q5R811, Q5T7P8, Q5XIS9, Q62746, Q6PFQ7, Q6PFY8, Q7TNM2, Q7TP90, Q7Z4K8, Q8BG60, Q8BHT7, Q8BQC3, Q8C6N3, Q8CIW5, Q8IZ69, Q8NCT1, Q920N2, Q92546, Q925B4

Diamond homologs: A0A0A2IBN3, A0A482NB13, A0KU76, A1RHE4, A1S4D3, A3D7B5, A4Y952, A6WR37, A8FSS4, A8H1S1, A9KYI1, B0RS27, B0TK00, B1KPU0, B2SHS9, B3H0C8, B8CJP2, B8E8S1, B8EI29, C5D4V7, G0FUS0, O31503, O58994, P0DO33, P0DXV1, P20187, P44074, P9WEU0, Q0HL77, Q0HXI0, Q12PZ8, Q1QUF2, Q2NSL7, Q2P2C4, Q3BSF8, Q3J8U2, Q4UVL4, Q5GZB5, Q67LE6, Q72HI4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	3
Likely pathogenic	1
Uncertain significance	90
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (4)

Variant ID	HGVS	Classification
1071026	NC_000022.10:g.(?18900688)(21351637_?)del	Pathogenic
1703643	GRCh37/hg19 22q11.21(chr22:18648866-21798907)	Pathogenic
685644	GRCh37/hg19 22q11.21(chr22:18916842-20311858)x1	Pathogenic
627510	Single allele	Likely pathogenic

SpliceAI

1915 predictions. Top by Δscore:

Variant	Effect	Δscore
22:20112790:AGAGG:A	acceptor_gain	1.0000
22:20112791:GAGG:G	acceptor_gain	1.0000
22:20112792:AGG:A	acceptor_gain	1.0000
22:20112793:GG:G	acceptor_gain	1.0000
22:20112795:C:CC	acceptor_gain	1.0000
22:20112907:TCACT:T	donor_loss	1.0000
22:20112908:CAC:C	donor_loss	1.0000
22:20112909:A:AC	donor_gain	1.0000
22:20112909:ACT:A	donor_gain	1.0000
22:20112909:ACTC:A	donor_gain	1.0000
22:20112910:C:CT	donor_gain	1.0000
22:20112910:CT:C	donor_gain	1.0000
22:20112910:CTC:C	donor_gain	1.0000
22:20112910:CTCC:C	donor_gain	1.0000
22:20112910:CTCCA:C	donor_gain	1.0000
22:20112912:C:CA	donor_gain	1.0000
22:20113003:GGAAT:G	acceptor_gain	1.0000
22:20113008:C:CC	acceptor_gain	1.0000
22:20113096:T:TA	donor_gain	1.0000
22:20113116:A:AC	donor_gain	1.0000
22:20113117:C:CC	donor_gain	1.0000
22:20113117:CG:C	donor_gain	1.0000
22:20113230:CAACT:C	acceptor_gain	1.0000
22:20113233:CT:C	acceptor_gain	1.0000
22:20113235:C:CC	acceptor_gain	1.0000
22:20113427:CTCA:C	donor_loss	1.0000
22:20113428:TCA:T	donor_loss	1.0000
22:20113429:CA:C	donor_loss	1.0000
22:20113430:A:AC	donor_gain	1.0000
22:20113430:A:AG	donor_loss	1.0000

AlphaMissense

4054 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
22:20114580:G:C	F409L	0.998
22:20114580:G:T	F409L	0.998
22:20114582:A:G	F409L	0.998
22:20112719:G:C	F574L	0.997
22:20112719:G:T	F574L	0.997
22:20112721:A:G	F574L	0.997
22:20115438:G:T	R240S	0.997
22:20116331:T:A	K102N	0.997
22:20116331:T:G	K102N	0.997
22:20116415:T:A	K74N	0.997
22:20116415:T:G	K74N	0.997
22:20113803:G:C	N413K	0.996
22:20113803:G:T	N413K	0.996
22:20115014:C:G	R319P	0.996
22:20115033:A:G	W313R	0.996
22:20115033:A:T	W313R	0.996
22:20115015:G:T	R319S	0.995
22:20115422:A:G	F245S	0.995
22:20116076:C:A	K187N	0.995
22:20116076:C:G	K187N	0.995
22:20116290:A:G	F116S	0.995
22:20116296:A:T	V114E	0.995
22:20115023:A:G	L316P	0.994
22:20116298:A:C	F113L	0.994
22:20116298:A:T	F113L	0.994
22:20116300:A:G	F113L	0.994
22:20116425:T:A	E71V	0.994
22:20113130:G:T	R513S	0.993
22:20115416:A:T	V247D	0.993
22:20115437:C:G	R240P	0.993

dbSNP variants (sampled 300 via entrez): RS1000172388 (22:20117260 C>A), RS1000722261 (22:20112872 G>A,C), RS1001019119 (22:20116097 A>G), RS1001068662 (22:20111718 C>A,G,T), RS1001770206 (22:20118049 C>G,T), RS1002133449 (22:20119017 C>G), RS1002288415 (22:20114416 G>A), RS1003003729 (22:20113872 C>G,T), RS1003317312 (22:20115611 C>A,G), RS1003428638 (22:20111651 G>A), RS1003517740 (22:20117386 G>A,T), RS1003746287 (22:20112953 T>C), RS1003959093 (22:20114151 A>G), RS1005017301 (22:20114460 T>A), RS1005305459 (22:20117545 G>A,C)

Disease associations

OMIM: gene MIM:611151 | disease phenotypes: MIM:188400

GenCC curated gene-disease

Mondo (1): DiGeorge syndrome (MONDO:0008564)

Orphanet (1): 22q11.2 deletion syndrome (Orphanet:567)

HPO phenotypes

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

GWAS associations

0 associations (top):

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
D004062	DiGeorge Syndrome	C05.660.207.103.500; C14.240.400.021.500; C14.280.400.044.500; C15.604.451.249.500; C16.131.077.019.500; C16.131.240.400.021.500; C16.131.260.019.500; C16.131.482.249.500; C16.131.621.207.103.500; C16.320.180.019.500; C19.642.482.500.500

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

15 total (human), top 15 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
aristolochic acid I	decreases expression	1
FR900359	increases phosphorylation	1
beta-lapachone	decreases expression	1
sodium arsenite	increases expression	1
di-n-butylphosphoric acid	affects expression	1
2-palmitoylglycerol	increases expression	1
jinfukang	affects cotreatment, increases expression	1
Sunitinib	increases expression	1
Acetaminophen	decreases expression	1
Cisplatin	affects cotreatment, increases expression	1
Doxorubicin	decreases expression	1
Enzyme Inhibitors	decreases activity, increases O-linked glycosylation	1
Smoke	decreases expression	1
Valproic Acid	increases methylation	1
Acrylamide	decreases expression	1

Cellosaurus cell lines

8 cell lines: 8 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_B2JR	Abcam HeLa TRMT2A KO	Cancer cell line	Female
CVCL_B8A4	Abcam Raji TRMT2A KO	Cancer cell line	Male
CVCL_C0AY	Abcam THP-1 TRMT2A KO	Cancer cell line	Male
CVCL_C7CL	Abcam PC-3 TRMT2A KO	Cancer cell line	Male
CVCL_TU76	HAP1 TRMT2A (-) 1	Cancer cell line	Male
CVCL_TU77	HAP1 TRMT2A (-) 2	Cancer cell line	Male
CVCL_TU78	HAP1 TRMT2A (-) 3	Cancer cell line	Male
CVCL_TU79	HAP1 TRMT2A (-) 4	Cancer cell line	Male

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT00395538	PHASE3	TERMINATED	Effects of PTH Replacement on Bone in Hypoparathyroidism
NCT00576407	PHASE2	COMPLETED	Thymus Transplantation in DiGeorge Syndrome #668
NCT00576836	PHASE2	COMPLETED	Thymus Transplantation Dose in DiGeorge #932
NCT01821781	PHASE2	ACTIVE_NOT_RECRUITING	Immune Disorder HSCT Protocol
NCT05149898	PHASE2	COMPLETED	Open-Label Study of ZYN002 Administered as a Transdermal Gel to Children and Adolescents With 22q11.2 Deletion Syndrome (INSPIRE)
NCT07284641	PHASE2	RECRUITING	Hematopoietic Stem Cell Transplantation (HSCT) for Common Variable Immunodeficiency (CVID) and Other Autoimmune Manifestations of Primary Immune Regulatory Disorders (PIRD)
NCT00566488	PHASE1	COMPLETED	Parathyroid and Thymus Transplantation in DiGeorge #931
NCT00579709	PHASE1	COMPLETED	Thymus Transplantation With Immunosuppression
NCT00849888	PHASE1	TERMINATED	Serum-Free Thymus Transplantation in DiGeorge Anomaly
NCT02895906	PHASE1	COMPLETED	Safety and Efficacy Study of NFC-1 in Subjects Aged 12-17 Years With 22q11.2DS & Associated Neuropsychiatric Conditions
NCT00579527	PHASE1/PHASE2	COMPLETED	Phase I/II Thymus Transplantation With Immunosuppression #950
NCT00004351	Not specified	COMPLETED	Study of Phenotype and Genotype Correlations in Patients With Contiguous Gene Deletion Syndromes
NCT00005102	Not specified	UNKNOWN	Immunologic Evaluation in Patients With DiGeorge Syndrome or Velocardiofacial Syndrome
NCT00105274	Not specified	COMPLETED	Velocardiofacial (VCFS; 22q11.2; DiGeorge) Syndrome Study
NCT00278005	Not specified	TERMINATED	Infection in DiGeorge Following CHD Surgery
NCT00556530	Not specified	RECRUITING	Examining Genetic Factors That Affect the Severity of 22q11.2 Deletion Syndrome
NCT00916955	Not specified	COMPLETED	Genetic Modifiers for 22q11.2 Syndrome
NCT01220531	Not specified	COMPLETED	Thymus Transplantation Safety-Efficacy
NCT01781923	Not specified	COMPLETED	Cognitive Remediation in 22q11DS
NCT02381457	Not specified	COMPLETED	SNP-based Microdeletion and Aneuploidy RegisTry (SMART)
NCT02430584	Not specified	UNKNOWN	Whole Blood Specimen Collection From Pregnant Subjects
NCT02460328	Not specified	COMPLETED	Resolution of Primary Immune Defect in 22q11.2 Deletion Syndrome
NCT02787486	Not specified	COMPLETED	Expanded Noninvasive Genomic Medical Assessment: The Enigma Study
NCT03284060	Not specified	TERMINATED	Social Cognition Training and Cognitive Remediation
NCT04141540	Not specified	COMPLETED	Molecular Variants Associated With Schizophrenia: Differential Analysis of Monozygotic Twins With Variable Phenotypic 22q11
NCT04373226	Not specified	TERMINATED	Arithmetic Abilities in Children With 22q11.2DS
NCT04639388	Not specified	RECRUITING	Understanding of Psychotic Disorders in Children With 22q11.2DS
NCT04639960	Not specified	TERMINATED	Neuroprotective Effects of Risperdal on Brain and Cognition in 22q11 Deletion Syndrome
NCT04647500	Not specified	COMPLETED	Effects of Methylphenidate on Brain and Cognition in 22q11 Deletion Syndrome
NCT05924347	Not specified	RECRUITING	Early Scoliotic Changes in Children at Increased Risk for Scoliosis Development
NCT07493096	Not specified	RECRUITING	Intensive Multimodal Neurorehabilitation Targeting Neuroplasticity in Pediatric Neurodevelopmental and Chromosomal Disorders