TRMT61A

Summary

TRMT61A (tRNA methyltransferase 61A, HGNC:23790) is a protein-coding gene on chromosome 14q32.33, encoding tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A (Q96FX7). Catalytic subunit of tRNA (adenine-N(1)-)-methyltransferase, which catalyzes the formation of N(1)-methyladenine at position 58 (m1A58) in initiator methionyl-tRNA. It is a selective cancer dependency (DepMap: 18.4% of cell lines).

Enables mRNA (adenine-N1-)-methyltransferase activity. Involved in mRNA processing. Part of tRNA (m1A) methyltransferase complex.

Source: NCBI Gene 115708 — RefSeq curated summary.

At a glance

• GWAS associations: 12
• Clinical variants (ClinVar): 46 total — 1 likely-pathogenic
• Cancer dependency (DepMap): dependent in 18.4% of screened cell lines
• MANE Select transcript: NM_152307

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23790
Approved symbol	TRMT61A
Name	tRNA methyltransferase 61A
Location	14q32.33
Locus type	gene with protein product
Status	Approved
Aliases	FLJ40452, GCD14, Gcd14p, hTRM61
Ensembl gene	ENSG00000166166
Ensembl biotype	protein_coding
OMIM	620885
Entrez	115708

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 11 protein_coding

ENST00000299202, ENST00000389749, ENST00000896880, ENST00000896881, ENST00000936559, ENST00000936560, ENST00000955301, ENST00000955302, ENST00000955303, ENST00000955304, ENST00000955305

RefSeq mRNA: 1 — MANE Select: NM_152307 NM_152307

CCDS: CCDS41994

Canonical transcript exons

ENST00000389749 — 4 exons

Exon	Start	End
ENSE00001100391	103532582	103532848
ENSE00001151679	103529950	103530309
ENSE00001699304	103534550	103537073
ENSE00001700387	103529196	103529261

Expression profiles

Bgee: expression breadth ubiquitous, 285 present calls, max score 94.01.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 9.6746 / max 112.3688, expressed in 1775 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
141747	6.0664	1746
141748	3.4153	1402
141749	0.1928	70

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
type B pancreatic cell	CL:0000169	94.01	silver quality
cervix squamous epithelium	UBERON:0006922	93.09	silver quality
olfactory bulb	UBERON:0002264	92.76	silver quality
parotid gland	UBERON:0001831	91.99	gold quality
tendon of biceps brachii	UBERON:0008188	91.27	silver quality
triceps brachii	UBERON:0001509	90.30	gold quality
right uterine tube	UBERON:0001302	88.99	gold quality
lower esophagus muscularis layer	UBERON:0035833	88.29	gold quality
lower esophagus	UBERON:0013473	88.24	gold quality
gluteal muscle	UBERON:0002000	87.90	gold quality
tongue squamous epithelium	UBERON:0006919	87.72	silver quality
muscle layer of sigmoid colon	UBERON:0035805	87.32	gold quality
cerebellar vermis	UBERON:0004720	87.31	silver quality
vena cava	UBERON:0004087	87.22	gold quality
cervix epithelium	UBERON:0004801	87.15	silver quality
esophagogastric junction muscularis propria	UBERON:0035841	86.86	gold quality
nasal cavity epithelium	UBERON:0005384	86.61	silver quality
upper arm skin	UBERON:0004263	86.57	gold quality
decidua	UBERON:0002450	86.14	gold quality
putamen	UBERON:0001874	85.90	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	85.81	gold quality
pancreatic ductal cell	CL:0002079	85.63	silver quality
nipple	UBERON:0002030	85.48	gold quality
subthalamic nucleus	UBERON:0001906	85.45	gold quality
cardia of stomach	UBERON:0001162	85.39	gold quality
saphenous vein	UBERON:0007318	85.26	gold quality
dorsal plus ventral thalamus	UBERON:0001897	85.23	gold quality
body of tongue	UBERON:0011876	85.22	gold quality
lateral nuclear group of thalamus	UBERON:0002736	84.89	gold quality
pylorus	UBERON:0001166	84.65	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.65

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

83 targeting TRMT61A, 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-6127	100.00	66.76	2188
HSA-MIR-6129	100.00	66.46	2080
HSA-MIR-3667-3P	99.99	67.17	1636
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-6721-5P	99.93	68.92	2981
HSA-MIR-4492	99.87	68.25	3611
HSA-MIR-221-5P	99.86	65.45	1052
HSA-MIR-8073	99.86	65.21	1118
HSA-MIR-4447	99.85	67.81	2900
HSA-MIR-6842-5P	99.80	67.54	1587
HSA-MIR-7110-5P	99.80	67.84	1712
HSA-MIR-6764-5P	99.75	67.89	2304
HSA-MIR-6752-3P	99.72	66.71	1587
HSA-MIR-6512-3P	99.65	66.07	1468
HSA-MIR-6720-5P	99.65	66.22	1459
HSA-MIR-4516	99.61	67.78	3390
HSA-MIR-6132	99.60	65.83	1554
HSA-MIR-6836-5P	99.60	65.62	1538
HSA-MIR-6752-5P	99.59	67.32	1243
HSA-MIR-762	99.58	66.61	1994
HSA-MIR-1915-3P	99.58	66.79	1988
HSA-MIR-6751-5P	99.56	64.99	1145
HSA-MIR-549A-3P	99.54	68.17	825
HSA-MIR-1207-5P	99.49	69.11	2983
HSA-MIR-4441	99.49	66.56	3216
HSA-MIR-4498	99.47	67.42	2360
HSA-MIR-1275	99.47	67.90	2749
HSA-MIR-3922-3P	99.25	64.96	1136
HSA-MIR-3176	99.25	64.35	954
HSA-MIR-6837-5P	99.25	65.47	1632

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 18.4% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 3)

• we suggest that PKCA tightly controls TRM6/61 activity to prevent translation deregulation that would favor neoplastic development. (PMID:26234676)
• The TRM61 heterotetramer is the only active species, both subunits are required for orientating tRNA for catalysis at Trm61. (PMID:26470919)
• N(1)-methyladenosine methylation in tRNA drives liver tumourigenesis by regulating cholesterol metabolism. (PMID:34728628)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	trmt61a	ENSDARG00000008480
mus_musculus	Trmt61a	ENSMUSG00000060950
rattus_norvegicus	Trmt61a	ENSRNOG00000011398
drosophila_melanogaster	Trmt61	FBGN0039407
caenorhabditis_elegans	W02A11.1	WBGENE00012192

Paralogs (1): TRMT61B (ENSG00000171103)

Protein

Protein identifiers

tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A — Q96FX7 (reviewed: Q96FX7)

Alternative names: mRNA methyladenosine-N(1)-methyltransferase catalytic subunit TRMT61A, tRNA(m1A58)-methyltransferase subunit TRMT61A

All UniProt accessions (2): Q96FX7, H0Y2Q1

UniProt curated annotations — full annotation on UniProt →

Function. Catalytic subunit of tRNA (adenine-N(1)-)-methyltransferase, which catalyzes the formation of N(1)-methyladenine at position 58 (m1A58) in initiator methionyl-tRNA. Catalytic subunit of mRNA N(1)-methyltransferase complex, which mediates methylation of adenosine residues at the N(1) position of a small subset of mRNAs: N(1) methylation takes place in tRNA T-loop-like structures of mRNAs and is only present at low stoichiometries.

Subunit / interactions. Heterotetramer; composed of two copies of TRMT6 and two copies of TRMT61A.

Subcellular location. Nucleus.

Similarity. Belongs to the class I-like SAM-binding methyltransferase superfamily. TRM61 family.

RefSeq proteins (1): NP_689520* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR014816	tRNA_MeTrfase_Gcd14	Family
IPR029063	SAM-dependent_MTases_sf	Homologous_superfamily
IPR049470	TRM61_C	Domain

Pfam: PF08704

Enzyme classification (BRENDA):

• EC 2.1.1.220 — tRNA (adenine58-N1)-methyltransferase (BRENDA: 8 organisms, 17 substrates, 2 inhibitors, 5 Km, 0 kcat entries)

Substrate kinetics (BRENDA)

3 substrates with measured Km, best-characterized 3. Km ranges are aggregated across organisms/conditions.

Substrate	Km (mM)	Measurements
ADENINE58 IN INITIATOR TRNAMET	—	1
ADENINE58 IN TRNAPHE	0.0001	1
S-ADENOSYL-L-METHIONINE	0.005	1

Catalyzed reactions (Rhea), 2 shown:

• adenosine(58) in tRNA + S-adenosyl-L-methionine = N(1)-methyladenosine(58) in tRNA + S-adenosyl-L-homocysteine + H(+) (RHEA:43152)
• an adenosine in mRNA + S-adenosyl-L-methionine = an N(1)-methyladenosine in mRNA + S-adenosyl-L-homocysteine + H(+) (RHEA:55392)

UniProt features (49 total): strand 16, binding site 14, helix 10, modified residue 2, turn 2, initiator methionine 1, chain 1, region of interest 1, sequence variant 1, compositionally biased region 1

Structure

Experimental structures (PDB)

3 structures.

PDB	Method	Resolution (Å)
5CCB	X-RAY DIFFRACTION	2
5CCX	X-RAY DIFFRACTION	2.1
5CD1	X-RAY DIFFRACTION	3.6

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96FX7-F1	92.78	0.79

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 (14): 114–116; 135; 140; 163–164; 180–183; 181; 205–212; 278; 20–22; 35–42; 64–65; 85–89 …

Post-translational modifications (2): 2, 263

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

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

MSigDB gene sets: 118 (showing top): GOBP_TRNA_METABOLIC_PROCESS, GOBP_RNA_METHYLATION, MONNIER_POSTRADIATION_TUMOR_ESCAPE_UP, PATIL_LIVER_CANCER, GOBP_RNA_MODIFICATION, DOANE_RESPONSE_TO_ANDROGEN_DN, GOBP_TRNA_METHYLATION, GARCIA_TARGETS_OF_FLI1_AND_DAX1_DN, GOBP_METHYLATION, chr14q32, GOBP_TRNA_PROCESSING, SHEN_SMARCA2_TARGETS_DN, REACTOME_METABOLISM_OF_RNA, GOBP_TRNA_MODIFICATION, GOCC_TRANSFERASE_COMPLEX

GO Biological Process (5): mRNA processing (GO:0006397), tRNA methylation (GO:0030488), RNA processing (GO:0006396), tRNA processing (GO:0008033), methylation (GO:0032259)

GO Molecular Function (5): mRNA (adenine-N1-)-methyltransferase activity (GO:0061953), tRNA (adenine(58)-N1)-methyltransferase activity (GO:0160107), protein binding (GO:0005515), methyltransferase activity (GO:0008168), transferase activity (GO:0016740)

GO Cellular Component (3): nucleus (GO:0005634), nucleoplasm (GO:0005654), tRNA (m1A) methyltransferase complex (GO:0031515)

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 processing	2
mRNA metabolic process	1
RNA methylation	1
tRNA modification	1
gene expression	1
RNA biosynthetic process	1
primary metabolic process	1
tRNA metabolic process	1
metabolic process	1
mRNA methyltransferase activity	1
tRNA (adenine) methyltransferase activity	1
binding	1
transferase activity, transferring one-carbon groups	1
catalytic activity	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
cellular anatomical structure	1
tRNA methyltransferase complex	1

Protein interactions and networks

STRING

1762 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TRMT61A	TRMT6	Q9UJA5	999
TRMT61A	TRMT61B	Q9BVS5	893
TRMT61A	TRMT10C	Q7L0Y3	821
TRMT61A	WDR4	P57081	744
TRMT61A	TRMT112	Q9UI30	728
TRMT61A	METTL1	Q9UBP6	726
TRMT61A	TRMT11	Q7Z4G4	718
TRMT61A	TRMT5	Q32P41	710
TRMT61A	FTSJ1	Q9UET6	710
TRMT61A	ALKBH1	Q13686	700
TRMT61A	ALKBH3	Q96Q83	670
TRMT61A	NSUN2	Q08J23	642
TRMT61A	TRMT10A	Q8TBZ6	631
TRMT61A	ADAT3	Q96EY9	626
TRMT61A	BUD23	O43709	625

IntAct

59 interactions, top by confidence:

A	B	Type	Score
SRP9	SRP72	psi-mi:“MI:0914”(association)	0.730
TRMT61A	TRMT6	psi-mi:“MI:0915”(physical association)	0.670
USE1	NBAS	psi-mi:“MI:0914”(association)	0.640
TCL1A	TRMT61A	psi-mi:“MI:0915”(physical association)	0.560
EMILIN1	METTL15	psi-mi:“MI:0914”(association)	0.530
TRMT61A	ARHGEF11	psi-mi:“MI:0914”(association)	0.530
ZNRD2	MYO9A	psi-mi:“MI:0914”(association)	0.530
EVL	VASP	psi-mi:“MI:0914”(association)	0.530
MAGEB2	GTPBP10	psi-mi:“MI:0914”(association)	0.530
JUN	TPM3	psi-mi:“MI:0914”(association)	0.350
ORF37	RPP40	psi-mi:“MI:0914”(association)	0.350
CAND1	GTPBP10	psi-mi:“MI:0914”(association)	0.350
COPS5	FBLL1	psi-mi:“MI:0914”(association)	0.350
CAMK2D	SETD1A	psi-mi:“MI:0914”(association)	0.350
EVL	RPL23	psi-mi:“MI:0914”(association)	0.350
DYRK3	EIF3F	psi-mi:“MI:0914”(association)	0.350
GRK4	TCERG1	psi-mi:“MI:0914”(association)	0.350
MYLK	ACOT7	psi-mi:“MI:0914”(association)	0.350
PLK3	AIP	psi-mi:“MI:0914”(association)	0.350
SNRK	PRPF6	psi-mi:“MI:0914”(association)	0.350
MAST1	ZSWIM8	psi-mi:“MI:0914”(association)	0.350
ATG2A	TTC4	psi-mi:“MI:0914”(association)	0.350
SSB	RPS3A	psi-mi:“MI:0914”(association)	0.350
	EIF3F	psi-mi:“MI:0914”(association)	0.350
	GTPBP10	psi-mi:“MI:0914”(association)	0.350
	ESYT2	psi-mi:“MI:0914”(association)	0.350
	POLR3A	psi-mi:“MI:0914”(association)	0.350

BioGRID (108): TRMT6 (Affinity Capture-MS), ARHGEF12 (Affinity Capture-MS), ARHGEF11 (Affinity Capture-MS), RBFOX2 (Affinity Capture-MS), PBLD (Affinity Capture-MS), FHL2 (Affinity Capture-MS), SKIV2L2 (Co-fractionation), TLN2 (Co-fractionation), TRMT6 (Co-fractionation), TRMT61A (Co-fractionation), TRMT61A (Co-fractionation), TRMT61A (Co-fractionation), TRMT61A (Co-fractionation), TRMT61A (Affinity Capture-MS), TRMT6 (Affinity Capture-MS)

ESM2 similar proteins: A0JNU3, A1A4L8, A2APY7, A2AV36, A5GFY8, A5GFZ6, A6H791, A7MBC0, A7YW45, B2GV71, B5DPF1, D4A1R8, O14744, O88202, O95396, O95571, P19623, P31754, P43353, Q28HC6, Q3KRD0, Q3T094, Q4QR99, Q4R5M3, Q5BJY6, Q5R698, Q5ZKI2, Q64674, Q66JK4, Q6AY46, Q6NS21, Q6NUA1, Q7SYK1, Q80XC2, Q86U10, Q8C166, Q8CIG8, Q8GWT4, Q8JZV7, Q96FX7

Diamond homologs: A6H791, A8AAV7, O14307, P0CS08, P0CS09, P46959, Q2U3W4, Q4WUT7, Q5A416, Q6AY46, Q6BX32, Q6C0P9, Q6CN53, Q6FL77, Q755M8, Q80XC2, Q86JJ0, Q96FX7, P9WFZ0, P9WFZ1, Q2YY85, Q57598, Q5SKN4, Q8GBB2, Q9BVS5, Q9V1J7, Q12UV0, A6LNM3, Q8TT94

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 63 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
SRP-dependent cotranslational protein targeting to membrane	6	13.1×	2e-03
Formation of a pool of free 40S subunits	5	12.2×	6e-03
L13a-mediated translational silencing of Ceruloplasmin expression	5	11.0×	6e-03
GTP hydrolysis and joining of the 60S ribosomal subunit	5	10.9×	6e-03
Major pathway of rRNA processing in the nucleolus and cytosol	6	8.1×	6e-03

GO biological processes:

GO term	Partners	Fold	FDR
cytoplasmic translation	5	15.4×	7e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	1
Uncertain significance	42
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
3747854	NM_152307.3(TRMT61A):c.665C>T (p.Ala222Val)	Likely pathogenic

SpliceAI

1419 predictions. Top by Δscore:

Variant	Effect	Δscore
14:103521819:TTCC:T	donor_gain	1.0000
14:103521946:CCGCC:C	acceptor_gain	1.0000
14:103521947:CGCC:C	acceptor_gain	1.0000
14:103521947:CGCCC:C	acceptor_gain	1.0000
14:103521949:CC:C	acceptor_gain	1.0000
14:103521950:CC:C	acceptor_gain	1.0000
14:103521951:C:CA	acceptor_loss	1.0000
14:103521951:C:CC	acceptor_gain	1.0000
14:103521951:C:T	acceptor_gain	1.0000
14:103521952:T:G	acceptor_loss	1.0000
14:103522017:CCGCA:C	donor_loss	1.0000
14:103522018:CGCA:C	donor_loss	1.0000
14:103522019:GCACC:G	donor_loss	1.0000
14:103522020:CA:C	donor_loss	1.0000
14:103522021:A:AT	donor_loss	1.0000
14:103522173:GTGGC:G	acceptor_gain	1.0000
14:103522174:TGGC:T	acceptor_gain	1.0000
14:103522175:GGC:G	acceptor_gain	1.0000
14:103522176:GC:G	acceptor_gain	1.0000
14:103522177:CC:C	acceptor_gain	1.0000
14:103522178:C:CC	acceptor_gain	1.0000
14:103522179:T:C	acceptor_loss	1.0000
14:103522191:C:CT	acceptor_gain	1.0000
14:103522295:GCGTA:G	donor_loss	1.0000
14:103522296:CGTAC:C	donor_loss	1.0000
14:103522297:GTAC:G	donor_loss	1.0000
14:103522298:TA:T	donor_loss	1.0000
14:103522299:A:AC	donor_gain	1.0000
14:103522299:A:AT	donor_loss	1.0000
14:103522299:AC:A	donor_gain	1.0000

AlphaMissense

1852 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
14:103532603:C:T	S118F	0.999
14:103532656:T:C	F136L	0.998
14:103532658:C:A	F136L	0.998
14:103532658:C:G	F136L	0.998
14:103532792:A:T	D181V	0.998
14:103532793:C:A	D181E	0.998
14:103532793:C:G	D181E	0.998
14:103534563:C:G	C204W	0.998
14:103534567:T:C	F206L	0.998
14:103534569:C:A	F206L	0.998
14:103534569:C:G	F206L	0.998
14:103532603:C:A	S118Y	0.997
14:103532779:G:C	A177P	0.997
14:103532792:A:C	D181A	0.997
14:103530298:T:A	V107D	0.996
14:103532594:G:A	G115D	0.996
14:103532783:T:A	V178D	0.996
14:103530204:T:A	W76R	0.995
14:103530204:T:C	W76R	0.995
14:103530300:T:C	C108R	0.995
14:103532590:A:C	S114R	0.995
14:103532592:T:A	S114R	0.995
14:103532592:T:G	S114R	0.995
14:103532791:G:C	D181H	0.995
14:103534578:C:G	C209W	0.995
14:103530233:G:C	Q85H	0.994
14:103530233:G:T	Q85H	0.994
14:103530235:T:C	I86T	0.994
14:103532642:T:C	L131P	0.994
14:103532693:T:C	F148S	0.994

dbSNP variants (sampled 300 via entrez): RS1000264732 (14:103533529 G>A,T), RS1000833590 (14:103529706 C>T), RS1000946114 (14:103529392 T>A), RS1000963646 (14:103529376 C>T), RS1001257891 (14:103537129 C>T), RS1001612874 (14:103532803 C>A), RS1001716205 (14:103527483 A>T), RS1001826922 (14:103537485 T>C), RS1001833989 (14:103528558 G>A), RS1002053277 (14:103528831 C>G,T), RS1002289492 (14:103534047 G>A), RS1002366949 (14:103534280 C>T), RS1002421517 (14:103529112 C>A), RS1002883862 (14:103536720 A>C), RS1003019125 (14:103531708 T>A)

Disease associations

OMIM: gene MIM:620885 | disease phenotypes: MIM:122470

GenCC curated gene-disease

Mondo (1): Cornelia de Lange syndrome (MONDO:0016033)

Orphanet (1): Cornelia de Lange syndrome (Orphanet:199)

HPO phenotypes

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

GWAS associations

12 associations (top):

Study	Trait	p-value
GCST002539_23	Schizophrenia	1.000000e-13
GCST004521_15	Autism spectrum disorder or schizophrenia	2.000000e-12
GCST004521_262	Autism spectrum disorder or schizophrenia	6.000000e-09
GCST004602_210	Mean corpuscular volume	1.000000e-12
GCST005316_539	Intelligence (MTAG)	2.000000e-09
GCST005951_9	Body mass index	4.000000e-09
GCST006077_4	Branched-chain amino acid levels (Isoleucine)	3.000000e-08
GCST007044_22	Extremely high intelligence	4.000000e-08
GCST010083_51	Hemoglobin levels	2.000000e-09
GCST010703_23	Brain morphology (MOSTest)	2.000000e-09
GCST90002392_466	Mean corpuscular volume	2.000000e-22
GCST90002403_472	Red blood cell count	1.000000e-14

EFO canonical traits (6, from GWAS)

EFO ID	Trait name
EFO:0004337	intelligence
EFO:0004340	body mass index
EFO:0005134	amino acid measurement
EFO:0004509	hemoglobin measurement
EFO:0004346	neuroimaging measurement
EFO:0004305	erythrocyte count

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
bisphenol A	affects cotreatment, affects expression, increases abundance, increases expression, decreases expression	4
sodium arsenite	decreases expression, increases expression	2
aristolochic acid I	increases expression	1
ginger extract	affects cotreatment, affects expression, increases abundance	1
2,4,6-tribromophenol	decreases expression	1
deoxynivalenol	increases expression	1
decabromobiphenyl ether	decreases expression	1
tetrabromobisphenol A	decreases expression	1
S-(1,2-dichlorovinyl)cysteine	increases expression, affects response to substance	1
abrine	increases expression	1
2,2’,4,4’-tetrabromodiphenyl ether	decreases expression	1
pentabrominated diphenyl ether 100	decreases expression	1
hexabrominated diphenyl ether 153	decreases expression	1
Temozolomide	increases expression	1
Sunitinib	increases expression	1
Arsenic Trioxide	decreases expression	1
Benzo(a)pyrene	affects methylation	1
Cisplatin	decreases expression	1
Dichlorodiphenyl Dichloroethylene	increases expression	1
Dexamethasone	affects cotreatment, increases expression	1
Estradiol	increases expression	1
Hydrogen Peroxide	affects cotreatment, decreases expression, increases expression	1
Indomethacin	increases expression, affects cotreatment	1
Ivermectin	decreases expression	1
Lipopolysaccharides	affects response to substance, increases expression	1
Oils, Volatile	affects cotreatment, affects expression, increases abundance	1
Ribonucleotides	affects binding	1
Silicon Dioxide	increases expression	1
Smoke	decreases expression	1
Theophylline	affects cotreatment, decreases expression	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT04381897	PHASE2	NOT_YET_RECRUITING	Use of N-Acetylcysteine in the Treatment of Repetitive and Self-Injurious Behaviors in Cornelia de Lange Syndrome
NCT06789783	PHASE2/PHASE3	RECRUITING	Cornelia De Lange Syndrome: Assessing Positive Effects of Lithium Treatment
NCT01793168	Not specified	RECRUITING	Rare Disease Patient Registry & Natural History Study - Coordination of Rare Diseases at Sanford
NCT03113877	Not specified	TERMINATED	Evaluation of Autonomic Function in Individuals With Cornelia de Lange Syndrome (CdLS)
NCT04463316	Not specified	RECRUITING	GROWing Up With Rare GENEtic Syndromes
NCT05829668	Not specified	RECRUITING	Behavioral Assessment and Treatment of Problem Behavior in Children With Cornelia de Lange Syndrome