WDR12

Summary

WDR12 (WD repeat domain 12, HGNC:14098) is a protein-coding gene on chromosome 2q33.2, encoding Ribosome biogenesis protein WDR12 (Q9GZL7). Component of the PeBoW complex, which is required for maturation of 28S and 5.8S ribosomal RNAs and formation of the 60S ribosome. It is a common-essential gene (DepMap: required in 98.6% of cancer cell lines).

This gene encodes a member of the WD repeat protein family. WD repeats are minimally conserved regions of approximately 40 amino acids typically bracketed by gly-his and trp-asp (GH-WD), which may facilitate formation of heterotrimeric or multiprotein complexes. Members of this family are involved in a variety of cellular processes, including cell cycle progression, signal transduction, apoptosis, and gene regulation. This protein is highly similar to the mouse WD repeat domain 12 protein at the amino acid level. The protein encoded by this gene is a component of a nucleolar protein complex that affects maturation of the large ribosomal subunit.

Source: NCBI Gene 55759 — RefSeq curated summary.

At a glance

• GWAS associations: 18
• Clinical variants (ClinVar): 73 total
• Druggable target: yes
• Cancer dependency (DepMap): dependent in 98.6% of screened cell lines (common-essential)
• MANE Select transcript: NM_018256

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:14098
Approved symbol	WDR12
Name	WD repeat domain 12
Location	2q33.2
Locus type	gene with protein product
Status	Approved
Aliases	YTM1, FLJ10881
Ensembl gene	ENSG00000138442
Ensembl biotype	protein_coding
OMIM	616620
Entrez	55759

Gene structure

Transcript identifiers

Ensembl transcripts: 15 — 8 protein_coding, 6 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000261015, ENST00000463824, ENST00000464820, ENST00000467777, ENST00000475611, ENST00000477723, ENST00000477727, ENST00000478869, ENST00000688520, ENST00000910663, ENST00000923857, ENST00000923858, ENST00000923859, ENST00000923860, ENST00000953982

RefSeq mRNA: 2 — MANE Select: NM_018256 NM_001371664, NM_018256

CCDS: CCDS2356

Canonical transcript exons

ENST00000261015 — 13 exons

Exon	Start	End
ENSE00000803452	202894581	202894626
ENSE00001076372	202882711	202882783
ENSE00001076374	202883609	202883741
ENSE00001076375	202884198	202884303
ENSE00001172562	202911436	202911673
ENSE00001881564	202874261	202880937
ENSE00002333522	202896065	202896219
ENSE00003515928	202899531	202899637
ENSE00003565352	202884395	202884535
ENSE00003595132	202897300	202897415
ENSE00003635658	202892617	202892702
ENSE00003665403	202901025	202901119
ENSE00003666898	202907865	202907959

Expression profiles

Bgee: expression breadth ubiquitous, 288 present calls, max score 96.33.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 26.7770 / max 354.5567, expressed in 1809 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
33291	19.9916	1779
33293	4.2579	1555
33292	1.6630	882
33290	0.7163	353
33297	0.1482	52

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
ventricular zone	UBERON:0003053	96.33	gold quality
ganglionic eminence	UBERON:0004023	95.43	gold quality
cortical plate	UBERON:0005343	95.00	gold quality
secondary oocyte	CL:0000655	94.87	gold quality
stromal cell of endometrium	CL:0002255	94.41	gold quality
embryo	UBERON:0000922	93.44	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	93.42	gold quality
buccal mucosa cell	CL:0002336	93.41	gold quality
mucosa of transverse colon	UBERON:0004991	93.23	gold quality
adrenal tissue	UBERON:0018303	93.15	gold quality
right adrenal gland	UBERON:0001233	92.69	gold quality
left adrenal gland	UBERON:0001234	92.51	gold quality
left adrenal gland cortex	UBERON:0035825	92.47	gold quality
right adrenal gland cortex	UBERON:0035827	92.39	gold quality
adrenal gland	UBERON:0002369	92.16	gold quality
choroid plexus epithelium	UBERON:0003911	92.08	gold quality
esophagus mucosa	UBERON:0002469	91.93	gold quality
adrenal cortex	UBERON:0001235	91.71	gold quality
gastrocnemius	UBERON:0001388	91.47	gold quality
hindlimb stylopod muscle	UBERON:0004252	91.45	gold quality
right atrium auricular region	UBERON:0006631	91.30	gold quality
muscle of leg	UBERON:0001383	91.29	gold quality
right testis	UBERON:0004534	91.15	gold quality
calcaneal tendon	UBERON:0003701	91.09	gold quality
left testis	UBERON:0004533	90.99	gold quality
heart left ventricle	UBERON:0002084	90.82	gold quality
colonic epithelium	UBERON:0000397	90.79	gold quality
rectum	UBERON:0001052	90.76	gold quality
cardiac ventricle	UBERON:0002082	90.71	gold quality
right lobe of liver	UBERON:0001114	90.68	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-CURD-112	yes	8.08
E-ANND-3	yes	7.54

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

24 targeting WDR12, 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-340-5P	100.00	72.50	4437
HSA-MIR-3064-3P	100.00	70.09	1254
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-539-5P	99.93	70.30	2855
HSA-MIR-380-3P	99.89	70.18	1978
HSA-MIR-579-3P	99.86	71.66	3628
HSA-MIR-664B-3P	99.84	71.65	3590
HSA-MIR-548AZ-5P	99.83	69.94	3230
HSA-MIR-548T-5P	99.83	69.91	3220
HSA-MIR-4495	99.82	72.08	3080
HSA-MIR-6762-3P	99.66	66.94	1188
HSA-MIR-3609	99.52	69.89	2587
HSA-MIR-548AH-5P	99.52	69.73	2626
HSA-MIR-216A-5P	99.50	68.02	1288
HSA-MIR-3123	99.47	67.15	2693
HSA-MIR-20A-3P	99.44	69.10	1575
HSA-MIR-4311	99.31	70.47	3041
HSA-MIR-3675-3P	99.09	67.70	968
HSA-MIR-3149	98.77	67.13	1639
HSA-MIR-4684-5P	98.29	67.99	1650
HSA-MIR-216B-5P	97.16	66.76	1126
HSA-MIR-3976	96.67	67.79	1187
HSA-MIR-597-3P	96.46	68.03	1035

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 98.6% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 6)

• WDR12 triggers accumulation of p53 in a p19ARF-independent manner in proliferating cells but not in quiescent cells. (PMID:16043514)
• Results describe the role of PeBoW-specific proteins Pes1, Bop1, and WDR12 in complex assembly and stability, nucleolar transport, and pre-ribosome association. (PMID:17353269)
• The DDX27 can interact specifically with the Pes1 and Bop1 but fulfils critical function(s) for proper 3’ end formation of 47S rRNA independently of the PeBoW-complex. (PMID:25825154)
• MI associated WDR12 allele was associated significantly with diastolic dysfunction and left atrial size. (PMID:25915632)
• Integrative genomic analyses identify WDR12 as a novel oncogene involved in glioblastoma. (PMID:32180229)
• circMIRIAF aggravates myocardial ischemia-reperfusion injury via targeting miR-544/WDR12 axis. (PMID:38795544)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	wdr12	ENSDARG00000003287
mus_musculus	Wdr12	ENSMUSG00000026019
rattus_norvegicus	Wdr12	ENSRNOG00000017340
drosophila_melanogaster	CG6724	FBGN0032298
caenorhabditis_elegans	wdr-12	WBGENE00018893

Paralogs (1): WDR37 (ENSG00000047056)

Protein

Protein identifiers

Ribosome biogenesis protein WDR12 — Q9GZL7 (reviewed: Q9GZL7)

Alternative names: WD repeat-containing protein 12

All UniProt accessions (2): Q9GZL7, Q53T99

UniProt curated annotations — full annotation on UniProt →

Function. Component of the PeBoW complex, which is required for maturation of 28S and 5.8S ribosomal RNAs and formation of the 60S ribosome.

Subunit / interactions. Component of the PeBoW complex, composed of BOP1, PES1 and WDR12. The complex is held together by BOP1, which interacts with PES1 via its N-terminal domain and with WDR12 via a high-affinity interaction between the seven-bladed beta-propeller domains of the 2 proteins. The PeBoW complex associates with the 66S pre-ribosome. Interacts (via UBL domain) with MDN1 (via VWFA/MIDAS domain).

Subcellular location. Nucleus. Nucleolus. Nucleoplasm.

Induction. By MYC.

Similarity. Belongs to the WD repeat WDR12/YTM1 family.

RefSeq proteins (2): NP_001358593, NP_060726* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001680	WD40_rpt	Repeat
IPR012972	NLE	Domain
IPR015943	WD40/YVTN_repeat-like_dom_sf	Homologous_superfamily
IPR019775	WD40_repeat_CS	Conserved_site
IPR020472	WD40_PAC1	Repeat
IPR028599	WDR12/Ytm1	Family
IPR036322	WD40_repeat_dom_sf	Homologous_superfamily

Pfam: PF00400, PF08154

UniProt features (61 total): strand 32, repeat 7, sequence variant 4, turn 4, region of interest 3, helix 3, modified residue 2, mutagenesis site 2, initiator methionine 1, chain 1, cross-link 1, sequence conflict 1

Structure

Experimental structures (PDB)

3 structures.

PDB	Method	Resolution (Å)
6P0Q	X-RAY DIFFRACTION	1.72
6N31	X-RAY DIFFRACTION	2.6
8FKY	ELECTRON MICROSCOPY	2.67

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9GZL7-F1	89.15	0.70

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 (3): 2, 415, 239

Mutagenesis-validated functional residues (2):

Position	Phenotype
76	reduces interaction with mdn1.
78	abolishes interaction with mdn1.

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-6791226	Major pathway of rRNA processing in the nucleolus and cytosol

MSigDB gene sets: 191 (showing top): GOBP_RIBOSOME_BIOGENESIS, TGCGCANK_UNKNOWN, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP, SHEPARD_CRASH_AND_BURN_MUTANT_UP, GRAESSMANN_APOPTOSIS_BY_SERUM_DEPRIVATION_UP, WEI_MYCN_TARGETS_WITH_E_BOX, MARTINEZ_RB1_TARGETS_UP, GOBP_MATURATION_OF_5_8S_RRNA_FROM_TRICISTRONIC_RRNA_TRANSCRIPT_SSU_RRNA_5_8S_RRNA_LSU_RRNA, GOBP_MATURATION_OF_LSU_RRNA, GOBP_REGULATION_OF_CELL_CYCLE, LYF1_01, GOBP_MATURATION_OF_5_8S_RRNA, GOBP_RIBONUCLEOPROTEIN_COMPLEX_BIOGENESIS, GOBP_RIBOSOMAL_LARGE_SUBUNIT_BIOGENESIS, IVANOVA_HEMATOPOIESIS_EARLY_PROGENITOR

GO Biological Process (7): maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000463), maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000466), Notch signaling pathway (GO:0007219), ribosomal large subunit biogenesis (GO:0042273), regulation of cell cycle (GO:0051726), rRNA processing (GO:0006364), ribosome biogenesis (GO:0042254)

GO Molecular Function (2): ribonucleoprotein complex binding (GO:0043021), protein binding (GO:0005515)

GO Cellular Component (5): nucleoplasm (GO:0005654), nucleolus (GO:0005730), preribosome, large subunit precursor (GO:0030687), PeBoW complex (GO:0070545), nucleus (GO:0005634)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
rRNA processing in the nucleus and cytosol	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
ribonucleoprotein complex biogenesis	2
ribosome biogenesis	2
nuclear lumen	2
maturation of LSU-rRNA	1
maturation of 5.8S rRNA	1
cell surface receptor signaling pathway	1
cell cycle	1
regulation of cellular process	1
RNA processing	1
rRNA metabolic process	1
protein-containing complex binding	1
binding	1
cellular anatomical structure	1
intracellular membraneless organelle	1
preribosome	1
nucleolus	1
90S preribosome	1
nuclear protein-containing complex	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

3226 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
WDR12	BOP1	Q14137	997
WDR12	PES1	O00541	988
WDR12	MDN1	Q9NU22	878
WDR12	RSL24D1	Q9UHA3	865
WDR12	EBNA1BP2	Q99848	853
WDR12	WDR74	Q6RFH5	796
WDR12	NIP7	Q9Y221	784
WDR12	GNL2	Q13823	773
WDR12	RPF2	Q9H7B2	772
WDR12	NSA2	O95478	770
WDR12	BRIX1	Q8TDN6	720
WDR12	NMD3	Q96D46	708
WDR12	GNL3	Q9BVP2	696
WDR12	PDCD11	Q14690	688
WDR12	COL9A2	Q14055	680
WDR12	NIFK	Q9BYG3	680

IntAct

68 interactions, top by confidence:

A	B	Type	Score
PES1	WDR12	psi-mi:“MI:0915”(physical association)	0.850
WDR12	PES1	psi-mi:“MI:0914”(association)	0.850
BOP1	PES1	psi-mi:“MI:0914”(association)	0.810
PES1	BOP1	psi-mi:“MI:0914”(association)	0.810
CUL4B	COPS2	psi-mi:“MI:0914”(association)	0.790
NPM1	MPHOSPH10	psi-mi:“MI:0914”(association)	0.610
BOP1	WDR12	psi-mi:“MI:0914”(association)	0.600
VHL	WDR12	psi-mi:“MI:0915”(physical association)	0.560
TARDBP	WDR12	psi-mi:“MI:0915”(physical association)	0.560
PES1	AP3B1	psi-mi:“MI:0914”(association)	0.530
WDR55	PES1	psi-mi:“MI:0914”(association)	0.530
IGHMBP2	THAP12	psi-mi:“MI:0914”(association)	0.530
N	NOP56	psi-mi:“MI:0914”(association)	0.530
CASQ2	PES1	psi-mi:“MI:0914”(association)	0.530
SRPK2	RRP9	psi-mi:“MI:0914”(association)	0.530
TMCO5A	WDR12	psi-mi:“MI:0915”(physical association)	0.400
RRP1B	ZNF785	psi-mi:“MI:0914”(association)	0.350
Mecom	ESYT2	psi-mi:“MI:0914”(association)	0.350
ESR1	ESYT2	psi-mi:“MI:0914”(association)	0.350

BioGRID (408): WDR12 (Affinity Capture-MS), WDR12 (Affinity Capture-MS), WDR12 (Affinity Capture-MS), WDR12 (Affinity Capture-MS), BRIX1 (Co-fractionation), CHMP7 (Co-fractionation), DDX19A (Co-fractionation), DDX54 (Co-fractionation), EBNA1BP2 (Co-fractionation), FTSJ3 (Co-fractionation), GTPBP4 (Co-fractionation), HNRNPDL (Co-fractionation), NOC3L (Co-fractionation), PUS1 (Co-fractionation), RPL4 (Co-fractionation)

ESM2 similar proteins: A5DL92, A7RHG8, A7TMF9, A8QB65, A8XL02, B0W517, B3MJV8, B3N534, B3RQN1, B4GT01, B4HWV6, B4JPT9, B4KKN1, B4LS78, B4MU54, B4P116, B4Q9T6, B5DG67, B7PY76, B8AP31, P49177, P49178, P61480, P91343, P93339, P93397, P93398, P93563, Q08E38, Q0VC24, Q10051, Q17BB0, Q29KQ0, Q40507, Q40687, Q5BJ90, Q5REE6, Q6CU59, Q6FKK3, Q6NX08

Diamond homologs: A0A223GEB2, A1CJY4, A1D7I5, A1L271, A2QEV8, A4R3M4, A4RDD7, A6H603, A7THX0, A8ILK1, B0XYC8, B3MJV8, B4HWV6, B4Q9T6, B6QC56, B8AP31, B8M0Q1, E3LB80, G0SC29, O14435, O14775, O35353, O45040, P11017, P16520, P17343, P18851, P23232, P26308, P29387, P29829, P36408, P49177, P49178, P52287, P54311, P54313, P61480, P62871, P62872

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 69 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
rRNA modification in the nucleus and cytosol	6	26.7×	8e-06
rRNA processing in the nucleus and cytosol	5	19.1×	2e-04
Major pathway of rRNA processing in the nucleolus and cytosol	12	17.6×	3e-10
rRNA processing	5	17.4×	2e-04
Formation of a pool of free 40S subunits	6	16.0×	1e-04
Peptide chain elongation	5	15.1×	4e-04
Viral mRNA Translation	5	15.1×	4e-04
PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA	5	14.9×	4e-04

GO biological processes:

GO term	Partners	Fold	FDR
ribosomal small subunit biogenesis	8	31.4×	3e-08
rRNA processing	11	26.9×	1e-10
cytoplasmic translation	5	16.0×	2e-03
translation	6	10.6×	2e-03

Disease & clinical

Cancer significance

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	53
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

5099 predictions. Top by Δscore:

Variant	Effect	Δscore
2:202882709:ACC:A	donor_gain	1.0000
2:202882710:CCC:C	donor_gain	1.0000
2:202882779:TACAA:T	acceptor_gain	1.0000
2:202882781:CAA:C	acceptor_gain	1.0000
2:202882784:C:CC	acceptor_gain	1.0000
2:202884300:CTGT:C	acceptor_gain	1.0000
2:202884304:C:CC	acceptor_gain	1.0000
2:202884536:C:CC	acceptor_gain	1.0000
2:202892613:TGACC:T	donor_loss	1.0000
2:202892614:GA:G	donor_loss	1.0000
2:202892615:A:AC	donor_gain	1.0000
2:202892615:A:T	donor_loss	1.0000
2:202892615:AC:A	donor_gain	1.0000
2:202892616:C:CC	donor_gain	1.0000
2:202892616:CC:C	donor_gain	1.0000
2:202892700:GGA:G	acceptor_gain	1.0000
2:202892703:C:CC	acceptor_gain	1.0000
2:202892705:G:C	acceptor_gain	1.0000
2:202892709:C:CT	acceptor_gain	1.0000
2:202892710:A:AC	acceptor_gain	1.0000
2:202892710:A:C	acceptor_gain	1.0000
2:202894701:T:TA	donor_gain	1.0000
2:202896064:CT:C	donor_gain	1.0000
2:202896216:CTAT:C	acceptor_gain	1.0000
2:202896217:TAT:T	acceptor_gain	1.0000
2:202896220:C:CC	acceptor_gain	1.0000
2:202897364:T:A	donor_gain	1.0000
2:202899520:T:C	donor_gain	1.0000
2:202899534:T:TA	donor_gain	1.0000
2:202901020:CT:C	donor_loss	1.0000

AlphaMissense

2772 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:202883622:A:G	W370R	1.000
2:202883622:A:T	W370R	1.000
2:202883682:A:G	W350R	1.000
2:202883682:A:T	W350R	1.000
2:202884216:A:G	W324R	1.000
2:202884216:A:T	W324R	1.000
2:202884458:A:C	S273R	1.000
2:202884458:A:T	S273R	1.000
2:202884460:T:G	S273R	1.000
2:202894618:A:C	S206R	1.000
2:202894618:A:T	S206R	1.000
2:202894620:T:G	S206R	1.000
2:202880924:C:T	G403E	0.999
2:202880926:A:C	S402R	0.999
2:202880926:A:T	S402R	0.999
2:202880928:T:G	S402R	0.999
2:202882725:A:G	W394R	0.999
2:202882725:A:T	W394R	0.999
2:202883620:C:A	W370C	0.999
2:202883620:C:G	W370C	0.999
2:202883640:C:G	D364H	0.999
2:202883648:C:T	G361E	0.999
2:202883652:A:G	S360P	0.999
2:202883657:A:G	L358P	0.999
2:202883680:C:A	W350C	0.999
2:202883680:C:G	W350C	0.999
2:202883700:A:G	W344R	0.999
2:202883700:A:T	W344R	0.999
2:202884220:T:A	R322S	0.999
2:202884220:T:G	R322S	0.999

dbSNP variants (sampled 300 via entrez): RS1000062238 (2:202880295 T>C), RS1000190725 (2:202906641 A>G), RS1000195099 (2:202873902 A>T), RS1000411836 (2:202880616 T>G), RS1000458841 (2:202903927 C>G,T), RS1000785151 (2:202891879 C>T), RS1000831628 (2:202885371 G>A), RS1000834470 (2:202904305 A>G), RS1000927011 (2:202905257 T>C), RS1001012531 (2:202879187 C>T), RS1001066268 (2:202877339 C>A), RS1001210475 (2:202899474 G>A,T), RS1001218860 (2:202891450 T>C), RS1001319710 (2:202892650 C>T), RS1001337158 (2:202886068 C>A,T)

Disease associations

OMIM: gene MIM:616620 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

18 associations (top):

Study	Trait	p-value
GCST000340_6	Myocardial infarction (early onset)	1.000000e-08
GCST000998_23	Coronary heart disease	1.000000e-09
GCST002287_4	Coronary artery disease or ischemic stroke	4.000000e-09
GCST002289_16	Coronary artery disease	2.000000e-08
GCST002290_11	Coronary artery disease or large artery stroke	3.000000e-08
GCST004787_49	Coronary artery disease (myocardial infarction, percutaneous transluminal coronary angioplasty, coronary artery bypass grafting, angina or chromic ischemic heart disease)	3.000000e-19
GCST010101_5	White matter hyperintensities	4.000000e-13
GCST010102_1	White matter integrity (fractional anisotropy)	7.000000e-08
GCST010102_2	White matter integrity (fractional anisotropy)	6.000000e-09
GCST010698_18	Subcortical volume (min-P)	1.000000e-08
GCST010699_69	Brain morphology (min-P)	9.000000e-20
GCST010700_6	Cortical thickness (MOSTest)	2.000000e-14
GCST010701_36	Cortical surface area (MOSTest)	2.000000e-24
GCST010702_146	Subcortical volume (MOSTest)	2.000000e-13
GCST010703_42	Brain morphology (MOSTest)	1.000000e-08
GCST012580_6	White matter hyperintensities	4.000000e-08
GCST90014122_1	Lacunar stroke	4.000000e-09
GCST90014123_1	Lacunar stroke	5.000000e-08

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0005665	white matter hyperintensity measurement
EFO:0004641	white matter integrity
EFO:0004346	neuroimaging measurement
EFO:0004840	cortical thickness

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL6067171 (SINGLE PROTEIN)

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

ChEMBL bioactivities

3 potent at pChembl≥5 of 4 total, top 3 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
8.92	Kd	1.206	nM	CHEMBL3752910
8.92	ED50	1.206	nM	CHEMBL3752910
5.40	Kd	4000	nM	CHEMBL6145044

PubChem BioAssay actives

1 with measured affinity, of 2 total; 1 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

Compound	Assay	Type	Value	Unit
4-methyl-3-[(1-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide	2149963: Binding affinity to human WDR12 incubated for 45 mins by Kinobead based pull down assay	kd	0.0012	uM

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, decreases expression, decreases methylation	3
bisphenol A	decreases expression	2
sodium arsenite	decreases expression, affects cotreatment, increases abundance, increases expression	2
Tretinoin	decreases expression	2
Aflatoxin B1	affects cotreatment, decreases expression, decreases methylation	2
FR900359	increases phosphorylation	1
TAK-243	increases sumoylation	1
dicrotophos	decreases expression	1
methylmercuric chloride	increases expression	1
alpha phellandrene	decreases expression	1
triphenyl phosphate	affects expression	1
deoxynivalenol	increases expression	1
cobaltous chloride	decreases expression	1
manganese chloride	increases abundance, increases expression, affects cotreatment	1
potassium chromate(VI)	affects cotreatment, decreases expression	1
beta-methylcholine	affects expression	1
epigallocatechin gallate	decreases expression, affects cotreatment	1
di-n-butylphosphoric acid	affects expression	1
perfluorooctane sulfonic acid	increases expression	1
CGP 52608	increases reaction, affects binding	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
ICG 001	increases expression	1
enzalutamide	affects expression	1
LDN 193189	affects cotreatment, decreases expression	1
picoxystrobin	decreases expression	1
(+)-JQ1 compound	decreases expression	1
Rosiglitazone	increases expression	1
Sunitinib	decreases expression	1
Arsenic Trioxide	increases expression	1
Acetaminophen	decreases expression	1

ChEMBL screening assays

5 unique, capped per target: 5 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL5653005	Binding	Binding affinity to human WDR12 incubated for 45 mins by Kinobead based pull down assay	NVP-BHG712: Effects of Regioisomers on the Affinity and Selectivity toward the EPHrin Family. — ChemMedChem

Cellosaurus cell lines

5 cell lines: 5 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_YJ25	MCF-7 shWDR12-4	Cancer cell line	Female
CVCL_YJ26	MDA-MB-231 shWDR12-4	Cancer cell line	Female
CVCL_YJ27	MDA-MB-468 shWDR12-4	Cancer cell line	Female
CVCL_YJ28	SK-BR-3 shWDR12-4	Cancer cell line	Female
CVCL_YJ29	ZR-75-1 shWDR12-4	Cancer cell line	Female

Clinical trials (associated diseases)

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