WBP11

Summary

WBP11 (WW domain binding protein 11, HGNC:16461) is a protein-coding gene on chromosome 12p12.3, encoding WW domain-binding protein 11 (Q9Y2W2). Activates pre-mRNA splicing. It is a common-essential gene (DepMap: required in 99.6% of cancer cell lines).

This gene encodes a nuclear protein, which colocalizes with mRNA splicing factors and intermediate filament-containing perinuclear networks. This protein has 95% amino acid sequence identity to the mouse Wbp11 protein. It contains two proline-rich regions that bind to the WW domain of Npw38, a nuclear protein, and thus this protein is also called Npw38-binding protein NpwBP. The Npw38-NpwBP complex may function as a component of an mRNA factory in the nucleus.

Source: NCBI Gene 51729 — RefSeq curated summary.

At a glance

• Gene–disease (curated): vertebral, cardiac, tracheoesophageal, renal, and limb defects (Strong, GenCC)
• GWAS associations: 1
• Clinical variants (ClinVar): 165 total — 10 pathogenic, 12 likely-pathogenic
• Phenotypes (HPO): 29
• Cancer dependency (DepMap): dependent in 99.6% of screened cell lines (common-essential)
• MANE Select transcript: NM_016312

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:16461
Approved symbol	WBP11
Name	WW domain binding protein 11
Location	12p12.3
Locus type	gene with protein product
Status	Approved
Aliases	NPWBP, SIPP1, PPP1R165, BUG13
Ensembl gene	ENSG00000084463
Ensembl biotype	protein_coding
OMIM	618083
Entrez	51729

Gene structure

Transcript identifiers

Ensembl transcripts: 17 — 14 protein_coding, 2 retained_intron, 1 nonsense_mediated_decay

ENST00000261167, ENST00000535328, ENST00000535638, ENST00000543316, ENST00000544764, ENST00000858075, ENST00000858076, ENST00000858077, ENST00000858078, ENST00000858079, ENST00000918140, ENST00000918141, ENST00000918142, ENST00000918143, ENST00000918144, ENST00000918145, ENST00000918146

RefSeq mRNA: 1 — MANE Select: NM_016312 NM_016312

CCDS: CCDS8666

Canonical transcript exons

ENST00000261167 — 12 exons

Exon	Start	End
ENSE00000722932	14794537	14794736
ENSE00000722971	14794971	14795104
ENSE00000722993	14796807	14797003
ENSE00000822107	14799635	14799728
ENSE00000936318	14790456	14790749
ENSE00000936319	14784582	14787498
ENSE00000999862	14788951	14789133
ENSE00002313134	14803352	14803478
ENSE00003506819	14793731	14793922
ENSE00003561464	14791169	14791270
ENSE00003670270	14800752	14800783
ENSE00003684547	14801320	14801428

Expression profiles

Bgee: expression breadth ubiquitous, 291 present calls, max score 96.31.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 55.1561 / max 861.2169, expressed in 1819 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
129854	54.5291	1818
129849	0.5420	216
129850	0.0851	31

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sural nerve	UBERON:0015488	96.31	gold quality
germinal epithelium of ovary	UBERON:0001304	95.64	gold quality
palpebral conjunctiva	UBERON:0001812	95.46	gold quality
ventricular zone	UBERON:0003053	95.40	gold quality
penis	UBERON:0000989	95.25	gold quality
amniotic fluid	UBERON:0000173	95.23	gold quality
type B pancreatic cell	CL:0000169	95.00	gold quality
adrenal tissue	UBERON:0018303	94.94	gold quality
islet of Langerhans	UBERON:0000006	94.93	gold quality
eye	UBERON:0000970	94.92	gold quality
adult organism	UBERON:0007023	94.67	gold quality
ganglionic eminence	UBERON:0004023	94.62	gold quality
calcaneal tendon	UBERON:0003701	94.53	gold quality
embryo	UBERON:0000922	94.40	gold quality
visceral pleura	UBERON:0002401	94.40	gold quality
colonic epithelium	UBERON:0000397	94.26	gold quality
parotid gland	UBERON:0001831	94.24	gold quality
substantia nigra pars reticulata	UBERON:0001966	94.01	gold quality
trigeminal ganglion	UBERON:0001675	93.97	gold quality
parietal pleura	UBERON:0002400	93.97	gold quality
lateral globus pallidus	UBERON:0002476	93.95	gold quality
sperm	CL:0000019	93.81	gold quality
superior surface of tongue	UBERON:0007371	93.78	gold quality
male germ cell	CL:0000015	93.76	gold quality
caput epididymis	UBERON:0004358	93.66	gold quality
gastrocnemius	UBERON:0001388	93.58	gold quality
urethra	UBERON:0000057	93.56	gold quality
superficial temporal artery	UBERON:0001614	93.54	gold quality
renal glomerulus	UBERON:0000074	93.48	gold quality
bone marrow cell	CL:0002092	93.47	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	8.80

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

66 targeting WBP11, 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-188-3P	100.00	68.76	1240
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-548AN	99.97	70.91	2817
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-493-5P	99.96	72.47	2382
HSA-MIR-4725-3P	99.96	69.53	2520
HSA-MIR-6780B-5P	99.96	69.60	2562
HSA-MIR-497-5P	99.92	71.83	2674
HSA-MIR-7-1-3P	99.91	71.53	4384
HSA-MIR-7-2-3P	99.91	71.40	4394
HSA-MIR-15A-5P	99.90	72.80	2787
HSA-MIR-15B-5P	99.90	72.78	2798
HSA-MIR-16-5P	99.90	72.80	2780
HSA-MIR-195-5P	99.90	72.81	2805
HSA-MIR-3671	99.90	73.04	3897
HSA-MIR-424-5P	99.89	71.90	2641
HSA-MIR-6838-5P	99.89	71.94	2690
HSA-MIR-4496	99.88	68.89	2236
HSA-MIR-4271	99.88	68.32	2244
HSA-MIR-130B-5P	99.83	68.50	1888
HSA-MIR-4420	99.82	70.08	1624
HSA-MIR-181B-2-3P	99.81	70.06	1646
HSA-MIR-181B-3P	99.81	70.06	1646
HSA-MIR-3156-3P	99.76	66.72	939
HSA-MIR-4719	99.73	72.10	3329
HSA-MIR-4699-3P	99.71	70.15	3142
HSA-MIR-4729	99.69	72.18	4233
HSA-MIR-12124	99.68	69.17	2700

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 99.6% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 3)

• SIPP1 is a positive regulator of pre-mRNA splicing that is regulated by nucleocytoplasmic shuttling (PMID:16162498)
• The WW domain belonging to polyglutamine tract-binding protein 1 (PQBP1) is of particular interest due to its direct involvement in several X chromosome-linked intellectual disabilities, including Golabi-Ito-Hall (GIH) syndrome, where a single point mutation (Y65C) correlates with the development of the disease. The mutant cannot bind to its natural ligand WBP11, which regulates mRNA processing (PMID:27456546)
• Heterozygous loss of WBP11 function causes multiple congenital defects in humans and mice. (PMID:33276377)

Cross-species orthologs

0 orthologs

Protein

Protein identifiers

WW domain-binding protein 11 — Q9Y2W2 (reviewed: Q9Y2W2)

Alternative names: Npw38-binding protein, SH3 domain-binding protein SNP70, Splicing factor that interacts with PQBP-1 and PP1

All UniProt accessions (3): Q9Y2W2, F5GXS9, F5H5G4

UniProt curated annotations — full annotation on UniProt →

Function. Activates pre-mRNA splicing. May inhibit PP1 phosphatase activity.

Subunit / interactions. Interacts with PPP1CA, PPP1CB and PPP1CC. Interacts via the PGR motif with PQBP1 in the nucleus. Interacts with the WW domains of WBP4.

Subcellular location. Nucleus. Cytoplasm.

Tissue specificity. Ubiquitous. Highly expressed in the heart, pancreas, kidney skeletal muscle, placenta and brain (at protein level). Weakly expressed in liver and lung.

Disease relevance. Vertebral, cardiac, tracheoesophageal, renal, and limb defects (VCTRL) [MIM:619227] An autosomal dominant disorder with incomplete penetrance and variable expressivity, characterized by cardiac, vertebral, tracheo-esophageal, renal and limb defects. Some patients also exhibit craniofacial abnormalities. The disease is caused by variants affecting the gene represented in this entry.

RefSeq proteins (1): NP_057396* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR019007	Wbp11/ELF5/Saf1_N	Domain

Pfam: PF09429

UniProt features (42 total): modified residue 12, compositionally biased region 11, region of interest 7, sequence variant 4, mutagenesis site 3, cross-link 2, chain 1, coiled-coil region 1, short sequence motif 1

Structure

Experimental structures (PDB)

4 structures.

PDB	Method	Resolution (Å)
9R3D	ELECTRON MICROSCOPY	3.12
7ABF	ELECTRON MICROSCOPY	3.9
7ABG	ELECTRON MICROSCOPY	7.8
9R8V	ELECTRON MICROSCOPY	8.5

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9Y2W2-F1	63.32	0.18

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 (14): 13, 181, 192, 236, 237, 279, 283, 353, 361, 364, 565, 600, 557, 572

Mutagenesis-validated functional residues (3):

Position	Phenotype
192	loss of pqbp1-binding; when associated with a-197 and a-198.
197	loss of pqbp1-binding; when associated with a-192 and a-198.
198	loss of pqbp1-binding; when associated with a-192 and a-197.

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

ID	Pathway
R-HSA-72163	mRNA Splicing - Major Pathway
R-HSA-9918481	Dengue Virus-Host Interactions

MSigDB gene sets: 243 (showing top): GOBP_RIBOSOME_BIOGENESIS, TGCTGCT_MIR15A_MIR16_MIR15B_MIR195_MIR424_MIR497, GCM_PPM1D, BONCI_TARGETS_OF_MIR15A_AND_MIR16_1, DEURIG_T_CELL_PROLYMPHOCYTIC_LEUKEMIA_DN, KORKOLA_EMBRYONAL_CARCINOMA_UP, REACTOME_PROCESSING_OF_CAPPED_INTRON_CONTAINING_PRE_MRNA, GOBP_RNA_SPLICING, REACTOME_MRNA_SPLICING, DODD_NASOPHARYNGEAL_CARCINOMA_UP, TIEN_INTESTINE_PROBIOTICS_24HR_UP, FISCHER_DREAM_TARGETS, MCCLUNG_COCAINE_REWARD_5D, BIDUS_METASTASIS_UP, KORKOLA_TERATOMA_UP

GO Biological Process (4): rRNA processing (GO:0006364), mRNA processing (GO:0006397), RNA splicing (GO:0008380), RNA processing (GO:0006396)

GO Molecular Function (4): single-stranded DNA binding (GO:0003697), RNA binding (GO:0003723), WW domain binding (GO:0050699), protein binding (GO:0005515)

GO Cellular Component (7): acrosomal vesicle (GO:0001669), nucleus (GO:0005634), nucleoplasm (GO:0005654), cytosol (GO:0005829), sperm principal piece (GO:0097228), sperm end piece (GO:0097229), cytoplasm (GO:0005737)

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
mRNA Splicing	1
Dengue Virus Infection	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	5
RNA processing	3
sperm flagellum	2
rRNA metabolic process	1
ribosome biogenesis	1
mRNA metabolic process	1
gene expression	1
RNA biosynthetic process	1
primary metabolic process	1
DNA binding	1
nucleic acid binding	1
protein domain specific binding	1
binding	1
secretory granule	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
cytoplasm	1
intracellular anatomical structure	1

Protein interactions and networks

STRING

1364 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
WBP11	PQBP1	O60828	826
WBP11	PPP1CB	P37140	519
WBP11	KIAA0825	Q8IV33	506
WBP11	WBP4	O75554	479
WBP11	TXNL4A	P83876	478
WBP11	PPP1CC	P36873	475
WBP11	NPW	Q8N729	462
WBP11	LCORL	Q8N3X6	447
WBP11	TUBGCP6	Q96RT7	434
WBP11	NRDE2	Q9H7Z3	413
WBP11	PIK3R1	P27986	408
WBP11	TEKTIP1	A6NCJ1	400
WBP11	RBMXL1	Q96E39	393
WBP11	RPUSD2	Q8IZ73	388
WBP11	PPP4R2	Q9NY27	383

IntAct

167 interactions, top by confidence:

A	B	Type	Score
WBP11	PPP1CA	psi-mi:“MI:0915”(physical association)	0.850
WBP11	PQBP1	psi-mi:“MI:0915”(physical association)	0.800
PQBP1	WBP11	psi-mi:“MI:0407”(direct interaction)	0.800
C5orf22	WBP11	psi-mi:“MI:0915”(physical association)	0.800
WBP11	PQBP1	psi-mi:“MI:0914”(association)	0.800
WBP11	C5orf22	psi-mi:“MI:0915”(physical association)	0.800
PPP1CB	CCDC85C	psi-mi:“MI:0914”(association)	0.750
PPP1CC	CCDC85C	psi-mi:“MI:0914”(association)	0.740
MCRS1	WBP11	psi-mi:“MI:0915”(physical association)	0.700
WBP11	MCRS1	psi-mi:“MI:0915”(physical association)	0.700
UBL5	SART1	psi-mi:“MI:0914”(association)	0.670
GRB2	WBP11	psi-mi:“MI:0915”(physical association)	0.670
WBP11	GRB2	psi-mi:“MI:0915”(physical association)	0.670
PPP1CA	CCDC85C	psi-mi:“MI:0914”(association)	0.670
NIPSNAP2	HSPD1	psi-mi:“MI:0914”(association)	0.610
WBP4	WBP11	psi-mi:“MI:0915”(physical association)	0.570
WBP11		psi-mi:“MI:0915”(physical association)	0.570

BioGRID (231): WBP11 (Two-hybrid), WBP11 (Two-hybrid), WBP11 (Two-hybrid), TESC (Two-hybrid), WBP11 (Affinity Capture-RNA), WBP11 (Affinity Capture-RNA), WBP11 (Affinity Capture-MS), WBP11 (Affinity Capture-MS), WBP11 (Affinity Capture-MS), WBP11 (Affinity Capture-MS), WBP11 (Two-hybrid), RTN4IP1 (Two-hybrid), WBP11 (Two-hybrid), C5orf22 (Two-hybrid), WBP11 (Two-hybrid)

ESM2 similar proteins: A0JNI5, A2AJT4, A2AQ19, A4IFB1, B1H1X4, D3ZTQ1, O43290, P35269, Q05519, Q12872, Q13435, Q3THK3, Q3UJB0, Q3UQU0, Q3USH5, Q4V7C9, Q53F19, Q568R1, Q5EA53, Q5HZB6, Q5PQQ2, Q5R539, Q5RAD5, Q5XIW8, Q5ZM19, Q66I22, Q6AY96, Q6DDA4, Q6GLZ8, Q6INH5, Q6ZPZ3, Q8BZR9, Q8CFC7, Q8K194, Q8N2M8, Q8N5F7, Q8TF01, Q8VHI6, Q8WVK2, Q923D5

Diamond homologs: G3CHK5, Q5PQQ2, Q6P0D5, Q923D5, Q9LV14, Q9Y2W2

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 142 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
Maturation of hRSV A proteins	5	39.6×	1e-05
mRNA Polyadenylation	15	13.7×	6e-11
SUMOylation of transcription cofactors	5	12.7×	3e-03
mRNA Splicing - Major Pathway	22	12.5×	1e-15
mRNA Splicing	10	11.4×	2e-06
Processing of Capped Intron-Containing Pre-mRNA	12	10.3×	3e-07
Dengue Virus-Host Interactions	17	8.1×	5e-09
Metabolism of RNA	13	5.6×	4e-05

GO biological processes:

GO term	Partners	Fold	FDR
alternative mRNA splicing, via spliceosome	5	27.0×	3e-04
RNA splicing, via transesterification reactions	5	25.0×	3e-04
regulation of alternative mRNA splicing, via spliceosome	7	13.7×	3e-04
RNA processing	7	12.3×	3e-04
positive regulation of transcription elongation by RNA polymerase II	5	12.0×	6e-03
mRNA splicing, via spliceosome	16	11.7×	4e-10
RNA splicing	10	7.1×	3e-04
mRNA processing	10	6.3×	6e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	10
Likely pathogenic	12
Uncertain significance	113
Likely benign	3
Benign	1

Top pathogenic / likely-pathogenic (22)

Variant ID	HGVS	Classification
2582227	NM_016312.3(WBP11):c.1521dup (p.Arg508fs)	Pathogenic
3332602	NM_016312.3(WBP11):c.585del (p.Gly196fs)	Pathogenic
4200220	NM_016312.3(WBP11):c.220_224del (p.Asn74fs)	Pathogenic
4528374	NM_016312.3(WBP11):c.836C>G (p.Ser279Ter)	Pathogenic
4531388	NM_016312.3(WBP11):c.680dup (p.Arg228fs)	Pathogenic
4759233	NM_016312.3(WBP11):c.403G>T (p.Glu135Ter)	Pathogenic
4819266	NM_016312.3(WBP11):c.163C>T (p.Arg55Ter)	Pathogenic
917483	NM_016312.3(WBP11):c.484C>T (p.Gln162Ter)	Pathogenic
917484	NM_016312.3(WBP11):c.1559dup (p.Gly521fs)	Pathogenic
917485	NM_016312.3(WBP11):c.688C>T (p.Arg230Ter)	Pathogenic
1308645	NM_016312.3(WBP11):c.331G>T (p.Glu111Ter)	Likely pathogenic
2627374	NM_016312.3(WBP11):c.251dup (p.Leu85fs)	Likely pathogenic
3899983	NM_016312.3(WBP11):c.724del (p.Gln242fs)	Likely pathogenic
3980647	NM_016312.3(WBP11):c.521+1G>A	Likely pathogenic
3980649	NM_016312.3(WBP11):c.190+1del	Likely pathogenic
4076308	NM_016312.3(WBP11):c.680del (p.Pro227fs)	Likely pathogenic
4292908	NM_016312.3(WBP11):c.722-1G>C	Likely pathogenic
4530836	NM_016312.3(WBP11):c.1171C>T (p.Gln391Ter)	Likely pathogenic
4819100	NM_016312.3(WBP11):c.247A>T (p.Lys83Ter)	Likely pathogenic
4819307	NM_016312.3(WBP11):c.271C>T (p.Arg91Cys)	Likely pathogenic
917482	NM_016312.3(WBP11):c.280C>T (p.Arg94Ter)	Likely pathogenic
917486	NM_016312.3(WBP11):c.612del (p.Gly205fs)	Likely pathogenic

SpliceAI

1351 predictions. Top by Δscore:

Variant	Effect	Δscore
12:14787496:TAC:T	acceptor_gain	1.0000
12:14787497:ACCT:A	acceptor_loss	1.0000
12:14787498:CCT:C	acceptor_loss	1.0000
12:14787499:C:CC	acceptor_gain	1.0000
12:14787499:CT:C	acceptor_loss	1.0000
12:14787500:T:A	acceptor_loss	1.0000
12:14788945:CATCA:C	donor_loss	1.0000
12:14788946:ATCAC:A	donor_loss	1.0000
12:14788947:TCAC:T	donor_loss	1.0000
12:14788948:CACC:C	donor_loss	1.0000
12:14788950:C:CG	donor_loss	1.0000
12:14789129:AGCTC:A	acceptor_gain	1.0000
12:14789131:CTC:C	acceptor_gain	1.0000
12:14789132:TC:T	acceptor_gain	1.0000
12:14789133:CC:C	acceptor_gain	1.0000
12:14789134:C:A	acceptor_loss	1.0000
12:14789134:C:CC	acceptor_gain	1.0000
12:14789134:C:T	acceptor_gain	1.0000
12:14790451:TTTAC:T	donor_loss	1.0000
12:14790452:TTAC:T	donor_loss	1.0000
12:14790453:TACCT:T	donor_loss	1.0000
12:14790454:ACCTG:A	donor_loss	1.0000
12:14790455:CCTG:C	donor_loss	1.0000
12:14790745:TTGAC:T	acceptor_gain	1.0000
12:14790746:TGAC:T	acceptor_gain	1.0000
12:14790747:GAC:G	acceptor_gain	1.0000
12:14790748:AC:A	acceptor_gain	1.0000
12:14790748:ACCT:A	acceptor_loss	1.0000
12:14790748:ACCTG:A	acceptor_gain	1.0000
12:14790749:CC:C	acceptor_gain	1.0000

AlphaMissense

4152 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
12:14787072:A:G	L640P	1.000
12:14787081:A:C	M637R	1.000
12:14787092:G:C	F633L	1.000
12:14787092:G:T	F633L	1.000
12:14787093:A:C	F633C	1.000
12:14787093:A:G	F633S	1.000
12:14787094:A:G	F633L	1.000
12:14787094:A:T	F633I	1.000
12:14787103:A:G	Y630H	1.000
12:14787112:C:G	D627H	1.000
12:14787243:A:G	L583P	1.000
12:14787243:A:T	L583Q	1.000
12:14787252:G:A	P580L	1.000
12:14787252:G:C	P580R	1.000
12:14787252:G:T	P580H	1.000
12:14787253:G:A	P580S	1.000
12:14787253:G:T	P580T	1.000
12:14787257:A:C	F578L	1.000
12:14787257:A:T	F578L	1.000
12:14787258:A:C	F578C	1.000
12:14787258:A:G	F578S	1.000
12:14787259:A:G	F578L	1.000
12:14787288:A:C	I568S	1.000
12:14787288:A:G	I568T	1.000
12:14787288:A:T	I568N	1.000
12:14787294:G:T	P566Q	1.000
12:14787295:G:A	P566S	1.000
12:14787300:G:T	A564D	1.000
12:14787306:A:C	I562S	1.000
12:14787306:A:G	I562T	1.000

dbSNP variants (sampled 300 via entrez): RS1000032688 (12:14789796 G>A), RS1000187686 (12:14791547 G>A), RS1000363809 (12:14795960 T>A,C), RS1000489400 (12:14790067 A>G), RS1000584591 (12:14796278 T>C), RS1000790751 (12:14794060 C>A,T), RS1000941692 (12:14789155 A>G), RS1001587940 (12:14794906 T>C), RS1001815611 (12:14788164 A>C), RS1001831836 (12:14800957 A>T), RS1001904540 (12:14793573 G>A), RS1002371344 (12:14792826 T>G), RS1002387648 (12:14793914 C>A,T), RS1002474405 (12:14800512 T>G), RS1002511128 (12:14786235 C>T)

Disease associations

OMIM: gene MIM:618083 | disease phenotypes: MIM:619227

GenCC curated gene-disease

Disease	Classification	Inheritance
vertebral, cardiac, tracheoesophageal, renal, and limb defects	Strong	Autosomal dominant

Mondo (1): vertebral, cardiac, tracheoesophageal, renal, and limb defects (MONDO:0030987)

Orphanet (0):

HPO phenotypes

29 total (29 of 29 shown, HPO-id order):

HPO	Term
HP:0000006	Autosomal dominant inheritance
HP:0000104	Renal agenesis
HP:0000122	Unilateral renal agenesis
HP:0000176	Submucous cleft hard palate
HP:0000252	Microcephaly
HP:0000278	Retrognathia
HP:0000337	Broad forehead
HP:0000369	Low-set ears
HP:0000384	Preauricular skin tag
HP:0000445	Wide nose
HP:0000453	Choanal atresia
HP:0000465	Webbed neck
HP:0000767	Pectus excavatum
HP:0000912	Sprengel anomaly
HP:0000957	Cafe-au-lait spot
HP:0000998	Hypertrichosis
HP:0001263	Global developmental delay
HP:0001357	Plagiocephaly
HP:0002032	Esophageal atresia
HP:0002162	Low posterior hairline
HP:0002247	Duodenal atresia
HP:0002575	Tracheoesophageal fistula
HP:0002949	Fused cervical vertebrae
HP:0003298	Spina bifida occulta
HP:0003316	Butterfly vertebrae
HP:0004322	Short stature
HP:0004467	Preauricular pit
HP:0007018	Attention deficit hyperactivity disorder
HP:0011623	Muscular ventricular septal defect

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST90020028_1901	Hip circumference adjusted for BMI	2.000000e-08

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0008039	BMI-adjusted hip circumference

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
FR900359	increases phosphorylation	1
bisphenol F	affects cotreatment, increases expression	1
dicrotophos	increases expression	1
bisphenol A	decreases expression	1
sodium arsenite	increases abundance, increases expression	1
benzo(e)pyrene	increases methylation	1
aflatoxin B2	increases methylation	1
coumarin	affects phosphorylation	1
di-n-butylphosphoric acid	affects expression	1
2,3,5-(triglutathion-S-yl)hydroquinone	increases ADP-ribosylation	1
CGP 52608	affects binding, increases reaction	1
ICG 001	decreases expression	1
abrine	increases expression	1
bisphenol S	affects expression	1
bisphenol AF	increases expression	1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid	decreases expression	1
Arsenic	increases abundance, increases expression	1
Benzo(a)pyrene	decreases methylation	1
Cadmium	increases abundance, decreases expression	1
Cisplatin	decreases expression	1
Dichlorodiphenyl Dichloroethylene	increases expression	1
Dexamethasone	affects cotreatment, increases expression	1
Indomethacin	increases expression, affects cotreatment	1
Ivermectin	decreases expression	1
Methapyrilene	increases methylation	1
Ribonucleotides	affects binding	1
Rotenone	increases expression	1
Dronabinol	increases expression	1
1-Methyl-3-isobutylxanthine	increases expression, affects cotreatment	1
Aflatoxin B1	decreases methylation	1

Clinical trials (associated diseases)

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