BCDIN3D

Summary

BCDIN3D (BCDIN3 domain containing RNA methyltransferase, HGNC:27050) is a protein-coding gene on chromosome 12q13.12, encoding RNA 5’-monophosphate methyltransferase (Q7Z5W3). O-methyltransferase that specifically monomethylates 5’-monophosphate of cytoplasmic histidyl tRNA (tRNA(His)), acting as a capping enzyme by protecting tRNA(His) from cleavage by DICER1. It is a selective cancer dependency (DepMap: 10.6% of cell lines).

This gene encodes an RNA methyltransferase which belongs to the rossmann fold methyltransferase family, and serves as a 5’-methylphosphate capping enzyme that is specific for cytoplasmic histidyl tRNA. The encoded protein contains an S-adenosylmethionine binding domain and uses the methyl group donor, S-adenosylmethionine. This gene is overexpressed in breast cancer cells, and is related to the tumorigenic phenotype and poor prognosis of breast cancer. The encoded protein is thought to promote the cellular invasion of breast cancer cells, by downregulating the expression of tumor suppressor miRNAs through the dimethylation of the 5-monophosphate of the corresponding precursor miRNAs.

Source: NCBI Gene 144233 — RefSeq curated summary.

At a glance

• GWAS associations: 35
• Clinical variants (ClinVar): 46 total
• Druggable target: yes
• Cancer dependency (DepMap): dependent in 10.6% of screened cell lines
• MANE Select transcript: NM_181708

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:27050
Approved symbol	BCDIN3D
Name	BCDIN3 domain containing RNA methyltransferase
Location	12q13.12
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000186666
Ensembl biotype	protein_coding
OMIM	619601
Entrez	144233

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 1 protein_coding, 1 retained_intron

ENST00000333924, ENST00000550861

RefSeq mRNA: 1 — MANE Select: NM_181708 NM_181708

CCDS: CCDS8790

Canonical transcript exons

ENST00000333924 — 2 exons

Exon	Start	End
ENSE00001339753	49836043	49839015
ENSE00001339756	49842854	49843106

Expression profiles

Bgee: expression breadth ubiquitous, 180 present calls, max score 81.79.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 6.5076 / max 71.7681, expressed in 1729 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
130861	5.8806	1716
130862	0.3626	157
130860	0.2644	100

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	81.79	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	79.34	gold quality
islet of Langerhans	UBERON:0000006	77.38	gold quality
pancreatic ductal cell	CL:0002079	77.35	silver quality
ileal mucosa	UBERON:0000331	76.96	silver quality
cortical plate	UBERON:0005343	75.47	gold quality
granulocyte	CL:0000094	74.07	gold quality
stromal cell of endometrium	CL:0002255	73.69	gold quality
pancreas	UBERON:0001264	73.32	gold quality
ventricular zone	UBERON:0003053	73.08	gold quality
body of pancreas	UBERON:0001150	72.29	gold quality
right adrenal gland	UBERON:0001233	72.18	gold quality
right adrenal gland cortex	UBERON:0035827	72.05	gold quality
ganglionic eminence	UBERON:0004023	71.89	gold quality
smooth muscle tissue	UBERON:0001135	71.86	gold quality
lymph node	UBERON:0000029	71.39	gold quality
prefrontal cortex	UBERON:0000451	71.38	gold quality
left adrenal gland	UBERON:0001234	70.97	gold quality
vermiform appendix	UBERON:0001154	70.82	gold quality
leukocyte	CL:0000738	70.76	gold quality
muscle of leg	UBERON:0001383	70.73	gold quality
gastrocnemius	UBERON:0001388	70.67	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	70.32	gold quality
right lobe of liver	UBERON:0001114	70.31	gold quality
left adrenal gland cortex	UBERON:0035825	70.30	gold quality
body of stomach	UBERON:0001161	70.28	gold quality
mucosa of transverse colon	UBERON:0004991	70.27	gold quality
lower esophagus	UBERON:0013473	70.23	gold quality
lower esophagus muscularis layer	UBERON:0035833	70.22	gold quality
monocyte	CL:0000576	70.18	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-CURD-53	yes	154.04
E-ANND-3	no	4.03

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

72 targeting BCDIN3D, 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-3924	100.00	72.09	2394
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-196A-5P	100.00	68.16	684
HSA-MIR-196B-5P	100.00	68.16	681
HSA-MIR-6870-5P	99.99	68.55	2115
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-5698	99.97	68.49	2029
HSA-MIR-4723-5P	99.97	68.70	2034
HSA-MIR-7111-5P	99.97	68.48	2062
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753
HSA-MIR-4778-3P	99.93	70.40	1818
HSA-MIR-3140-3P	99.88	68.47	2069
HSA-LET-7A-2-3P	99.87	70.53	1921
HSA-LET-7G-3P	99.85	70.43	1929
HSA-MIR-4447	99.85	67.81	2900
HSA-MIR-4428	99.73	66.41	1733
HSA-MIR-3714	99.71	70.74	2671
HSA-MIR-4756-3P	99.62	66.30	1319
HSA-MIR-4472	99.56	66.08	1478
HSA-MIR-4761-5P	99.51	66.69	804
HSA-MIR-5571-5P	99.49	66.99	1764
HSA-MIR-4325	99.49	72.20	1342
HSA-MIR-6727-3P	99.49	65.92	1333
HSA-MIR-548G-3P	99.48	68.67	2159

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 10.6% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 8)

• BCDIN3D depletion leads to lower pre-miR-145 and concomitantly increased mature miR-145 levels in breast cancer cells, which suppresses their tumorigenic phenotypes. (PMID:23063121)
• BCDIN3D might serve as an important prognostic factor for triple-negative breast cancer (PMID:27259993)
• BCDIN3D acts as a cytoplasmic tRNAHis-specific 5-methylphosphate capping enzyme. (PMID:28119416)
• Human BCDIN3D monomethylates the 5’-monophosphate of cytoplasmic tRNAHis in vitro. In BCDN3D-knockout cells, established byCRISPR/Cas9 editing, the methyl moiety at the 5’-monophosphate of cytoplasmic tRNAHis is lost, and the exogenous expression of BCDIN3D in the knockout cells restores the modification in cytoplasmic tRNAHis. (PMID:28119416)
• Results indicate that tRNAHis interaction with BCDIN3D plays non-canonical roles, one of which is to regulate the generation of tRNAHis 3’ fragments. (PMID:31329584)
• CDIN3D is a tRNAHis-specific 5’-monomethylphosphate capping enzyme that discriminates tRNAHis from other tRNA species, and the structural information presented in this study also provides the molecular basis for the development of drugs against breast cancers. (PMID:31919512)
• MiR-195-3p inhibits cell proliferation in cervical cancer by targeting BCDIN3D. (PMID:33157501)
• BCDIN3D RNA methyltransferase stimulates Aldolase C expression and glycolysis through let-7 microRNA in breast cancer cells. (PMID:33664453)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	bcdin3d	ENSDARG00000074111
mus_musculus	Bcdin3d	ENSMUSG00000037525
rattus_norvegicus	Bcdin3d	ENSRNOG00000058430
drosophila_melanogaster	CG11342	FBGN0035537

Paralogs (1): MEPCE (ENSG00000146834)

Protein

Protein identifiers

RNA 5’-monophosphate methyltransferase — Q7Z5W3 (reviewed: Q7Z5W3)

Alternative names: BCDIN3 domain-containing protein

All UniProt accessions (1): Q7Z5W3

UniProt curated annotations — full annotation on UniProt →

Function. O-methyltransferase that specifically monomethylates 5’-monophosphate of cytoplasmic histidyl tRNA (tRNA(His)), acting as a capping enzyme by protecting tRNA(His) from cleavage by DICER1. Also able, with less efficiently, to methylate the 5’ monophosphate of a subset of pre-miRNAs, acting as a negative regulator of miRNA processing. The 5’ monophosphate of pre-miRNAs is recognized by DICER1 and is required for pre-miRNAs processing: methylation at this position reduces the processing of pre-miRNAs by DICER1. Was also reported to mediate dimethylation of pre-miR-145; however dimethylation cannot be reproduced by another group which observes a monomethylation of pre-miR-145.

Subunit / interactions. Interacts with DICER1; the interaction may be mediated by RNA.

Subcellular location. Cytoplasm.

Similarity. Belongs to the methyltransferase superfamily.

RefSeq proteins (1): NP_859059* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR010675	Bin3_C	Domain
IPR024160	BIN3_SAM-bd_dom	Domain
IPR029063	SAM-dependent_MTases_sf	Homologous_superfamily
IPR039772	Bin3-like	Family

Pfam: PF06859

Enzyme classification (BRENDA):

• EC 2.1.1.B140 — (BRENDA: organisms, substrates, inhibitors, Km, kcat entries)

Catalyzed reactions (Rhea), 2 shown:

• a 5’-end 5’-phospho-ribonucleoside-RNA + 2 S-adenosyl-L-methionine = a 5’-end (5’-bismethylphospho)-ribonucleoside-RNA + 2 S-adenosyl-L-homocysteine (RHEA:58640)
• a 5’-end 5’-phospho-ribonucleoside-RNA + S-adenosyl-L-methionine = a 5’-end (5’-methylphospho)-ribonucleoside-RNA + S-adenosyl-L-homocysteine (RHEA:58656)

UniProt features (57 total): mutagenesis site 25, helix 13, strand 9, binding site 5, chain 1, domain 1, region of interest 1, turn 1, sequence variant 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
6L8U	X-RAY DIFFRACTION	2.92

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q7Z5W3-F1	84.99	0.65

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 (5): 46; 76; 110; 135–136; 164

Mutagenesis-validated functional residues (25):

Position	Phenotype
46	abolished o-methyltransferase activity.
72–74	abolished o-methyltransferase activity.
72	abolished o-methyltransferase activity.
74	abolished o-methyltransferase activity.
76	abolished o-methyltransferase activity.
110	abolished o-methyltransferase activity.
111	decreased o-methyltransferase activity.
118	slightly decreased o-methyltransferase activity.
135	decreased o-methyltransferase activity.
136	abolished o-methyltransferase activity.
165	decreased o-methyltransferase activity.
166	decreased o-methyltransferase activity.
169	abolished o-methyltransferase activity.
198	abolished o-methyltransferase activity.
201–204	abolished o-methyltransferase activity.
201	decreased o-methyltransferase activity.
204	decreased o-methyltransferase activity.
208–209	abolished o-methyltransferase activity.
208	strongly decreased o-methyltransferase activity.
209	abolished o-methyltransferase activity.
211–212	abolished o-methyltransferase activity.
211	abolished o-methyltransferase activity.
212	decreased o-methyltransferase activity.
257	abolished o-methyltransferase activity.
37	abolished o-methyltransferase activity.

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

ID	Pathway
R-HSA-203927	MicroRNA (miRNA) biogenesis
R-HSA-211000	Gene Silencing by RNA
R-HSA-74160	Gene expression (Transcription)

MSigDB gene sets: 113 (showing top): GOBP_TRNA_METABOLIC_PROCESS, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GOBP_RNA_METHYLATION, GOBP_POST_TRANSCRIPTIONAL_REGULATION_OF_GENE_EXPRESSION, GOBP_RNA_MODIFICATION, GGAANCGGAANY_UNKNOWN, GOBP_TRNA_METHYLATION, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_5, NRF2_01, GOBP_PRE_MIRNA_PROCESSING, GOBP_METHYLATION, CETS1P54_01, GOBP_TRNA_PROCESSING, GOBP_TRNA_MODIFICATION, SCGGAAGY_ELK1_02

GO Biological Process (6): RNA methylation (GO:0001510), miRNA metabolic process (GO:0010586), tRNA methylation (GO:0030488), pre-miRNA processing (GO:0031054), negative regulation of pre-miRNA processing (GO:2000632), methylation (GO:0032259)

GO Molecular Function (8): O-methyltransferase activity (GO:0008171), RNA methyltransferase activity (GO:0008173), tRNA methyltransferase activity (GO:0008175), pre-miRNA binding (GO:0070883), small RNA 2’-O-ribose methyltransferase activity (GO:0090486), protein binding (GO:0005515), methyltransferase activity (GO:0008168), transferase activity (GO:0016740)

GO Cellular Component (4): nucleoplasm (GO:0005654), cytoplasm (GO:0005737), cytosol (GO:0005829), plasma membrane (GO:0005886)

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
Gene Silencing by RNA	1
Gene expression (Transcription)	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	3
methyltransferase activity	2
RNA modification	1
macromolecule methylation	1
RNA metabolic process	1
RNA methylation	1
tRNA modification	1
miRNA processing	1
pre-miRNA processing	1
negative regulation of miRNA processing	1
regulation of pre-miRNA processing	1
metabolic process	1
catalytic activity, acting on RNA	1
RNA methyltransferase activity	1
catalytic activity, acting on a tRNA	1
RNA binding	1
RNA 2’-O-methyltransferase activity	1
binding	1
transferase activity, transferring one-carbon groups	1
catalytic activity	1
nuclear lumen	1
intracellular anatomical structure	1
cytoplasm	1
membrane	1
cell periphery	1

Protein interactions and networks

STRING

622 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
BCDIN3D	FAIM2	Q9BWQ8	765
BCDIN3D	SEC16B	Q96JE7	691
BCDIN3D	KCTD15	Q96SI1	646
BCDIN3D	GNPDA2	Q8TDQ7	645
BCDIN3D	SH2B1	Q9NRF2	598
BCDIN3D	TMEM18	Q96B42	597
BCDIN3D	MTCH2	Q9Y6C9	582
BCDIN3D	NEGR1	Q7Z3B1	571
BCDIN3D	BIN3	Q9NQY0	568
BCDIN3D	DICER1	Q9UPY3	558
BCDIN3D	SETD7	Q8WTS6	503
BCDIN3D	FTO	Q9C0B1	478
BCDIN3D	MC4R	P32245	477
BCDIN3D	PRMT3	O60678	470
BCDIN3D	METTL1	Q9UBP6	463

IntAct

9 interactions, top by confidence:

A	B	Type	Score
RELL2	OXSR1	psi-mi:“MI:0914”(association)	0.830
BCDIN3D	ZFP2	psi-mi:“MI:0915”(physical association)	0.560
ZFP2	BCDIN3D	psi-mi:“MI:0915”(physical association)	0.560
SIX2	EYA2	psi-mi:“MI:0914”(association)	0.530
BCDIN3D	ACACB	psi-mi:“MI:0915”(physical association)	0.400
CUL3	PXDNL	psi-mi:“MI:0914”(association)	0.350
SIX2	EYA4	psi-mi:“MI:0914”(association)	0.350

BioGRID (11): BCDIN3D (Two-hybrid), BCDIN3D (Affinity Capture-MS), BCDIN3D (Affinity Capture-RNA), BCDIN3D (Affinity Capture-MS), BCDIN3D (Affinity Capture-MS), ACACB (Affinity Capture-MS), BCDIN3D (Affinity Capture-MS), BCDIN3D (Affinity Capture-MS), BCDIN3D (Affinity Capture-MS), BCDIN3D (Affinity Capture-RNA), BCDIN3D (Affinity Capture-MS)

ESM2 similar proteins: A0A5F8AH41, A1A4L5, A2AV36, A5WVX1, A8E7D2, B3DLB3, C0IN03, D4ABH7, D9IVE5, O43709, P0C5J1, P0DPD7, P0DPE0, P0DPE1, P10937, P10938, P11086, P40935, Q06AU9, Q07G10, Q29S19, Q32PY6, Q3T0H0, Q3UY23, Q3UZW7, Q501S4, Q5M8E6, Q5RFI3, Q6NTR1, Q6P4Z6, Q6PCI6, Q7T0L7, Q7Z5W3, Q7ZVS8, Q80Y20, Q80Y81, Q8BMK1, Q8BWQ4, Q8CAE2, Q8CGS5

Diamond homologs: A3KQ55, D4ABH7, Q29S19, Q5RFI3, Q6NPC9, Q7K480, Q7L2J0, Q7T0L7, Q7Z5W3, Q8K3A9, Q91YP1, Q9U2R0, Q9VNH1, Q9VZD2, A8E7D2

SIGNOR signaling

0 interactions.

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	0
Uncertain significance	38
Likely benign	3
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

151 predictions. Top by Δscore:

Variant	Effect	Δscore
12:49842849:CTCA:C	donor_loss	0.9900
12:49842850:TCAC:T	donor_loss	0.9900
12:49842851:CACCC:C	donor_loss	0.9900
12:49842852:ACC:A	donor_gain	0.9900
12:49842853:C:G	donor_loss	0.9900
12:49842853:CCC:C	donor_gain	0.9900
12:49842847:CACT:C	donor_loss	0.9800
12:49842848:ACTC:A	donor_loss	0.9800
12:49842852:A:AC	donor_gain	0.9800
12:49842852:AC:A	donor_gain	0.9800
12:49842853:C:CC	donor_gain	0.9800
12:49842853:CC:C	donor_gain	0.9800
12:49842906:T:A	donor_gain	0.9800
12:49839058:A:T	acceptor_gain	0.9700
12:49842845:GTCAC:G	donor_loss	0.9700
12:49842846:TCACT:T	donor_loss	0.9700
12:49842853:CCCCG:C	donor_gain	0.9700
12:49842852:ACCC:A	donor_gain	0.9400
12:49842853:CCCC:C	donor_gain	0.9400
12:49838970:C:CT	acceptor_gain	0.9000
12:49838970:C:T	acceptor_gain	0.9000
12:49839013:ATCC:A	acceptor_loss	0.9000
12:49839014:TCC:T	acceptor_loss	0.9000
12:49839015:CCTA:C	acceptor_loss	0.9000
12:49839016:C:A	acceptor_loss	0.9000
12:49839017:T:G	acceptor_loss	0.9000
12:49839028:A:T	acceptor_loss	0.8800
12:49842841:C:A	donor_gain	0.8700
12:49839016:C:CC	acceptor_gain	0.8400
12:49839052:T:TG	acceptor_gain	0.8400

AlphaMissense

1914 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
12:49839007:A:C	S81R	0.995
12:49839007:A:T	S81R	0.995
12:49839009:T:G	S81R	0.995
12:49838745:A:G	W169R	0.990
12:49838745:A:T	W169R	0.990
12:49842986:A:C	F34L	0.989
12:49842986:A:T	F34L	0.989
12:49842988:A:G	F34L	0.989
12:49838735:A:G	L172P	0.988
12:49842968:G:C	F40L	0.988
12:49842968:G:T	F40L	0.988
12:49842970:A:G	F40L	0.988
12:49838743:C:A	W169C	0.985
12:49838743:C:G	W169C	0.985
12:49838465:A:G	F262S	0.982
12:49838776:A:C	F158L	0.982
12:49838776:A:T	F158L	0.982
12:49838778:A:G	F158L	0.982
12:49838857:A:C	F131L	0.982
12:49838857:A:T	F131L	0.982
12:49838859:A:G	F131L	0.982
12:49838739:G:C	H171D	0.980
12:49838763:A:G	C163R	0.980
12:49842855:C:A	G78V	0.979
12:49838633:G:T	A206D	0.978
12:49838479:T:A	R257S	0.977
12:49838479:T:G	R257S	0.977
12:49838480:C:G	R257T	0.977
12:49838663:T:A	E196V	0.977
12:49838926:G:C	C108W	0.977

dbSNP variants (sampled 300 via entrez): RS1000020027 (12:49837181 G>A), RS1000120556 (12:49844336 A>G), RS1000339377 (12:49842888 G>A), RS1000393141 (12:49842553 C>G), RS1001322209 (12:49837293 T>TG), RS1002074336 (12:49840527 T>C), RS1002203245 (12:49836423 C>G), RS1002881457 (12:49840576 G>C), RS1003691244 (12:49842347 G>A), RS1003918623 (12:49840760 G>A), RS1004147105 (12:49842173 C>A,T), RS1004214744 (12:49839854 A>C), RS1004374024 (12:49840465 A>T), RS1004837088 (12:49840208 T>C), RS1005236425 (12:49844543 A>C)

Disease associations

OMIM: gene MIM:619601 | disease phenotypes: MIM:157900

GenCC curated gene-disease

Mondo (1): Mobius syndrome (MONDO:0008006)

Orphanet (1): Moebius syndrome (Orphanet:570)

HPO phenotypes

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

GWAS associations

35 associations (top):

Study	Trait	p-value
GCST000296_11	Body mass index	1.000000e-07
GCST000299_3	Weight	2.000000e-07
GCST000427_6	Waist circumference	8.000000e-07
GCST002541_93	Menarche (age at onset)	2.000000e-12
GCST002783_157	Body mass index	8.000000e-24
GCST002783_210	Body mass index	5.000000e-26
GCST002783_461	Body mass index	2.000000e-17
GCST002783_562	Body mass index	6.000000e-11
GCST003993_4	Menarche (age at onset)	1.000000e-08
GCST004065_105	Waist circumference	2.000000e-15
GCST004065_65	Waist circumference	9.000000e-12
GCST004065_94	Waist circumference	8.000000e-07
GCST004557_103	Body mass index	6.000000e-12
GCST004557_204	Body mass index	2.000000e-11
GCST004557_21	Body mass index	5.000000e-16
GCST004557_233	Body mass index	9.000000e-15
GCST004557_65	Body mass index	1.000000e-06
GCST004558_100	Body mass index (joint analysis main effects and physical activity interaction)	4.000000e-11
GCST004558_136	Body mass index (joint analysis main effects and physical activity interaction)	4.000000e-06
GCST004558_153	Body mass index (joint analysis main effects and physical activity interaction)	6.000000e-14
GCST004558_174	Body mass index (joint analysis main effects and physical activity interaction)	2.000000e-11
GCST004558_18	Body mass index (joint analysis main effects and physical activity interaction)	1.000000e-15
GCST004559_132	Body mass index in physically active individuals	1.000000e-09
GCST004559_16	Body mass index in physically active individuals	2.000000e-11
GCST004559_52	Body mass index in physically active individuals	1.000000e-08
GCST004559_98	Body mass index in physically active individuals	1.000000e-10
GCST004560_20	Body mass index in physically inactive individuals	2.000000e-06
GCST004560_44	Body mass index in physically inactive individuals	8.000000e-06
GCST004904_166	Body mass index	2.000000e-21
GCST005830_105	Hand grip strength	1.000000e-11

EFO canonical traits (6, from GWAS)

EFO ID	Trait name
EFO:0004340	body mass index
EFO:0004338	body weight
EFO:0004703	age at menarche
EFO:0008002	physical activity measurement
EFO:0006941	grip strength measurement
EFO:0000195	metabolic syndrome

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
D020331	Mobius Syndrome	C07.465.299.825; C10.292.319.825; C10.292.562.700.375.750; C11.590.436.400.750; C16.131.077.578; C16.614.595

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL3588740 (SINGLE PROTEIN)

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

ChEMBL bioactivities

570 potent at pChembl≥5 of 585 total, top 50 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
8.34	IC50	4.62	nM	CHEMBL5436586
8.21	IC50	6.1	nM	CHEMBL5413030
8.21	IC50	6.1	nM	CHEMBL5415042
8.21	IC50	6.1	nM	CHEMBL5438358
8.10	IC50	8	nM	CHEMBL5436795
7.86	IC50	13.9	nM	CHEMBL5432793
7.85	IC50	14	nM	CHEMBL5404773
7.84	IC50	14.4	nM	CHEMBL5432793
7.77	IC50	17	nM	CHEMBL5413152
7.77	IC50	17	nM	CHEMBL5436795
7.68	IC50	20.67	nM	CHEMBL5414651
7.66	IC50	21.7	nM	CHEMBL5418361
7.66	IC50	21.8	nM	CHEMBL5404773
7.62	IC50	24	nM	CHEMBL5395461
7.59	IC50	25.6	nM	CHEMBL5396743
7.59	IC50	25.8	nM	CHEMBL5417536
7.57	IC50	27	nM	CHEMBL5395461
7.56	IC50	27.8	nM	CHEMBL5426579
7.55	IC50	28	nM	CHEMBL5437313
7.55	IC50	28.4	nM	CHEMBL5409071
7.54	IC50	28.6	nM	CHEMBL5428172
7.52	IC50	29.9	nM	CHEMBL5421954
7.48	IC50	33.3	nM	CHEMBL5412120
7.48	IC50	33.4	nM	CHEMBL5406803
7.47	IC50	34.1	nM	CHEMBL5421954
7.47	IC50	34	nM	CHEMBL5413152
7.44	IC50	36.1	nM	CHEMBL5424258
7.42	IC50	38.5	nM	CHEMBL5428789
7.42	IC50	38.1	nM	CHEMBL5394381
7.42	IC50	38	nM	CHEMBL5414639
7.42	IC50	38.5	nM	CHEMBL5399891
7.41	IC50	39	nM	CHEMBL5419599
7.40	IC50	39.8	nM	CHEMBL5409304
7.39	IC50	40.8	nM	CHEMBL5411060
7.39	IC50	40.8	nM	CHEMBL5396743
7.38	IC50	41.7	nM	CHEMBL5399891
7.37	IC50	42.8	nM	CHEMBL5396303
7.37	IC50	42.8	nM	CHEMBL5437091
7.35	IC50	45	nM	CHEMBL5427210
7.35	IC50	44.4	nM	CHEMBL5413030
7.33	IC50	46.6	nM	CHEMBL5409361
7.33	IC50	47	nM	CHEMBL5426579
7.33	IC50	46.3	nM	CHEMBL5411060
7.33	IC50	47	nM	CHEMBL5438358
7.33	IC50	47.1	nM	CHEMBL5409071
7.30	IC50	50	nM	CHEMBL5425295
7.30	IC50	50.5	nM	CHEMBL5396955
7.30	IC50	50.12	nM	CHEMBL5414798
7.29	IC50	50.7	nM	CHEMBL5397822
7.29	IC50	50.7	nM	CHEMBL5422318

CTD chemical–gene interactions

29 total (human), top 29 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	increases expression, affects cotreatment	2
Valproic Acid	affects expression, increases expression	2
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
GSK-J4	decreases expression	1
methylmercuric chloride	decreases expression	1
triphenyl phosphate	affects expression	1
trichostatin A	increases expression	1
ferrous chloride	decreases expression	1
beta-methylcholine	affects expression	1
avobenzone	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
cylindrospermopsin	increases expression	1
bisphenol S	affects cotreatment, increases expression	1
(+)-JQ1 compound	increases expression	1
Temozolomide	increases expression	1
Air Pollutants	decreases expression, increases abundance	1
Arsenic	increases methylation	1
Atrazine	decreases expression	1
Benzo(a)pyrene	increases methylation	1
Dexamethasone	affects cotreatment, increases expression	1
Doxorubicin	affects expression	1
Indomethacin	affects cotreatment, increases expression	1
Ribonucleotides	affects binding	1
Tretinoin	decreases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, increases expression	1
Cyclosporine	decreases expression	1
Lactic Acid	decreases expression	1
Acrylamide	increases expression	1
Particulate Matter	decreases expression, increases abundance	1

ChEMBL screening assays

27 unique, capped per target: 27 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL3592418	Binding	Inhibition of BCDIN3D (unknown origin) assessed as incorporation of tritium labeled methyl group from [3H]-SAM to substrate at 1 uM after 1 hr by scintillation proximity assay relative to control	Discovery of A-893, A New Cell-Active Benzoxazinone Inhibitor of Lysine Methyltransferase SMYD2. — ACS Med Chem Lett

Cellosaurus cell lines

3 cell lines: 3 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_E1RX	HAP1 BCDIN3D (-) 2	Cancer cell line	Male
CVCL_E1RY	HAP1 BCDIN3D (-) 3	Cancer cell line	Male
CVCL_XL98	HAP1 BCDIN3D (-) 1	Cancer cell line	Male

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT03059420	Not specified	RECRUITING	Genetic Studies of Strabismus, Congenital Cranial Dysinnervation Disorders (CCDDs), and Their Associated Anomalies