NKX2-3

Summary

NKX2-3 (NK2 homeobox 3, HGNC:7836) is a protein-coding gene on chromosome 10q24.2, encoding Homeobox protein Nkx-2.3 (Q8TAU0). Transcription factor.

This gene encodes a homeodomain-containing transcription factor. The encoded protein is a member of the NKX family of homeodomain transcription factors. Studies of similar proteins in mouse and rat have indicated a potential role in cellular differentiation.

Source: NCBI Gene 159296 — RefSeq curated summary.

At a glance

• Gene–disease (curated): inflammatory bowel disease (Limited, GenCC)
• GWAS associations: 35
• Clinical variants (ClinVar): 45 total
• MANE Select transcript: NM_145285

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:7836
Approved symbol	NKX2-3
Name	NK2 homeobox 3
Location	10q24.2
Locus type	gene with protein product
Status	Approved
Aliases	NKX2.3, CSX3, NKX4-3
Ensembl gene	ENSG00000119919
Ensembl biotype	protein_coding
OMIM	606727
Entrez	159296

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000344586

RefSeq mRNA: 1 — MANE Select: NM_145285 NM_145285

CCDS: CCDS41558

Canonical transcript exons

ENST00000344586 — 2 exons

Exon	Start	End
ENSE00001316027	99534985	99536524
ENSE00001452880	99532942	99533489

Expression profiles

Bgee: expression breadth broad, 69 present calls, max score 90.42.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.4904 / max 72.5230, expressed in 75 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
106489	0.4298	72
106490	0.0606	20

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
muscle layer of sigmoid colon	UBERON:0035805	90.42	gold quality
spleen	UBERON:0002106	88.58	gold quality
small intestine Peyer’s patch	UBERON:0003454	84.12	gold quality
colon	UBERON:0001155	83.45	gold quality
small intestine	UBERON:0002108	83.30	gold quality
transverse colon	UBERON:0001157	83.11	gold quality
large intestine	UBERON:0000059	83.07	gold quality
intestine	UBERON:0000160	82.85	gold quality
duodenum	UBERON:0002114	80.60	gold quality
sural nerve	UBERON:0015488	80.39	gold quality
minor salivary gland	UBERON:0001830	79.58	gold quality
jejunal mucosa	UBERON:0000399	78.81	gold quality
mucosa of transverse colon	UBERON:0004991	78.66	gold quality
mouth mucosa	UBERON:0003729	77.24	gold quality
caecum	UBERON:0001153	75.61	gold quality
rectum	UBERON:0001052	73.57	gold quality
mucosa of sigmoid colon	UBERON:0004993	71.94	gold quality
vermiform appendix	UBERON:0001154	71.79	gold quality
pylorus	UBERON:0001166	71.75	gold quality
saliva-secreting gland	UBERON:0001044	71.69	gold quality
colonic epithelium	UBERON:0000397	71.40	gold quality
colonic mucosa	UBERON:0000317	71.15	gold quality
jejunum	UBERON:0002115	70.23	gold quality
cardia of stomach	UBERON:0001162	67.85	gold quality
gall bladder	UBERON:0002110	63.68	gold quality
body of stomach	UBERON:0001161	63.61	gold quality
body of pancreas	UBERON:0001150	63.57	gold quality
stomach	UBERON:0000945	62.75	gold quality
pancreas	UBERON:0001264	62.38	gold quality
fundus of stomach	UBERON:0001160	62.16	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.21

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

2 targets.

Target	Regulation
EGR1	Unknown
MADCAM1	Activation

JASPAR motifs

Motif	Name	Family
MA0672.1	NKX2-3	NK
MA0672.2	NKX2-3	NK

JASPAR matrix evidence (PMIDs): PMID:11042197

Upstream regulators (CollecTRI, top): NFATC1, NFATC2

miRNA regulators (miRDB)

26 targeting NKX2-3, 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-190A-3P	100.00	80.35	5520
HSA-MIR-5193	100.00	67.26	1744
HSA-MIR-32-5P	99.98	75.21	1964
HSA-MIR-92A-3P	99.98	75.21	1960
HSA-MIR-92B-3P	99.98	75.25	1955
HSA-MIR-25-3P	99.98	74.60	1817
HSA-MIR-363-3P	99.98	74.72	1821
HSA-MIR-367-3P	99.98	74.83	1819
HSA-MIR-6845-3P	99.94	66.88	1439
HSA-MIR-552-5P	99.93	68.56	1583
HSA-MIR-205-5P	99.81	70.05	1557
HSA-MIR-4319	99.76	69.83	2586
HSA-MIR-3618	99.69	68.57	1012
HSA-MIR-5001-3P	98.91	67.28	1394
HSA-MIR-487A-5P	98.85	69.37	993
HSA-MIR-487B-5P	98.85	69.48	987
HSA-MIR-6804-3P	98.72	64.82	852
HSA-MIR-2467-3P	98.65	67.18	1969
HSA-MIR-500A-3P	97.60	67.48	595
HSA-MIR-558	97.50	67.16	977
HSA-MIR-6886-3P	96.96	66.36	844
HSA-MIR-4695-3P	96.71	67.21	836
HSA-MIR-644A	96.02	66.52	786
HSA-MIR-6805-5P	95.79	64.86	670
HSA-MIR-6851-3P	95.73	65.11	688
HSA-MIR-1238-3P	95.27	62.25	552

Literature-anchored findings (GeneRIF, showing 20)

• Single nucleotide polymorphism in NKX2-3 gene is associated with Crohn’s disease and ulcerative colitis (PMID:18438405)
• A positive association signal presumably common to different ethnic groups for rs10883365 was detected in the upstream region of NKX2-3. (PMID:18936107)
• no evidence of association with celiac disease has been reported for the Crohn’s disease susceptibility polymorphisms studied in the NKX2-3, ATG16L1, and IRGM genes. (PMID:19683022)
• Nkx2-3 may contribute to the pathogenesis of inflammatory bowel disease-associated colorectal cancer and sporadic colorectal cancer by regulating the Wnt signaling pathway. (PMID:20165982)
• a decrease in Nkx2-3 gene expression level can profoundly alter the expression of genes and cellular functions relevant to the pathogenesis and progression of inflammatory bowel disease, such as EDN1. (PMID:20188614)
• Data suggest that NKX2-3 and IRGM are susceptibility loci for inflammatory bowel disease in Eastern European patients. (PMID:21049557)
• the risk haplotype of NKX2.3 confers susceptibility to UC through increasing expression of NKX2.3 mRNA in the colonic mucosa. (PMID:21514341)
• NKX2-3 may play an important role in inflammatory bowel disease pathogenesis by regulating endothelin-1 and VEGF signaling in human intestinal microvascular endothelial cells. (PMID:21637825)
• The binding of NFAT1 to the NKX2-3 promoter region with rs1190140 was confirmed by chromatin immunoprecipitation assay. (PMID:21803625)
• NKX2-3 may play different roles in ulcerative colitis and Crohn’s disease pathogenesis by differential regulation of EGR1. (PMID:21968973)
• A positive correlation was observed between mRNA expression of PTPN2 and NKX2-3 in B cells and in intestinal tissues from both Crohn’s disease and ulcerative colitis patients. (PMID:22377701)
• The persons with a NKX2-3 G or T allele may have a moderately increased risk of CD. (PMID:24473197)
• NKX2-3 is a key mediator for maintaining myofibroblast characteristics, and our results show that colorectal myofibroblasts, as defined by the expression of AOC3, NKX2-3, and other markers, are a distinctly different cell type from TGFbeta-activated fibroblasts (PMID:27036009)
• Studies suggest oncogenic NK2 homeobox 3 homeobox protein (NKX2-3) in lymphomagenesis, and show a mouse model for studying the biology and therapy of human marginal-zone B-cell lymphomas. (PMID:27297662)
• Mutations in RPSA and NKX2-3 link development of the spleen and intestinal vasculature. (PMID:31498527)
• Identification of novel, clonally stable, somatic mutations targeting transcription factors PAX5 and NKX2-3, the epigenetic regulator LRIF1, and BRAF in a case of atypical B-cell chronic lymphocytic leukemia harboring a t(14;18)(q32;q21). (PMID:33608382)
• Development and Validation of an Autophagy-Related Signature for Head and Neck Squamous Cell Carcinoma. (PMID:34423028)
• NKL Homeobox Genes NKX2-3 and NKX2-4 Deregulate Megakaryocytic-Erythroid Cell Differentiation in AML. (PMID:34768865)
• Transcription factor Nkx2-3 maintains the self-renewal of hematopoietic stem cells by regulating mitophagy. (PMID:37095209)
• Quantitative Analysis of NKX2-3 Expression in Human Colon: An Immunohistochemical Study. (PMID:38063211)

Cross-species orthologs

10 orthologs

Organism	Symbol	Gene ID
danio_rerio	nkx2.3	ENSDARG00000039095
mus_musculus	Nkx2-3	ENSMUSG00000044220
rattus_norvegicus	Nkx2-3	ENSRNOG00000016656
drosophila_melanogaster	NK7.1	FBGN0024321
drosophila_melanogaster	HGTX	FBGN0040318
drosophila_melanogaster	scro	FBGN0287186
caenorhabditis_elegans	ceh-9	WBGENE00000434
caenorhabditis_elegans		WBGENE00000447
caenorhabditis_elegans		WBGENE00000450
caenorhabditis_elegans		WBGENE00000584

Paralogs (13): NKX3-2 (ENSG00000109705), NKX2-4 (ENSG00000125816), NKX2-2 (ENSG00000125820), NKX2-8 (ENSG00000136327), NKX2-1 (ENSG00000136352), NKX6-2 (ENSG00000148826), NKX6-1 (ENSG00000163623), NKX6-3 (ENSG00000165066), NKX3-1 (ENSG00000167034), NKX2-6 (ENSG00000180053), NKX2-5 (ENSG00000183072), NKX1-2 (ENSG00000229544), NKX1-1 (ENSG00000235608)

Protein

Protein identifiers

Homeobox protein Nkx-2.3 — Q8TAU0 (reviewed: Q8TAU0)

Alternative names: Homeobox protein NK-2 homolog C

All UniProt accessions (1): Q8TAU0

UniProt curated annotations — full annotation on UniProt →

Function. Transcription factor.

Subcellular location. Nucleus.

Similarity. Belongs to the NK-2 homeobox family.

RefSeq proteins (1): NP_660328* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001356	HD	Domain
IPR009057	Homeodomain-like_sf	Homologous_superfamily
IPR017970	Homeobox_CS	Conserved_site
IPR020479	HD_metazoa	Domain
IPR050394	Homeobox_NK-like	Family

Pfam: PF00046

UniProt features (4 total): chain 1, DNA-binding region 1, region of interest 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8TAU0-F1	60.75	0.18

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 137 (showing top): GOBP_MYELOID_CELL_DIFFERENTIATION, GOBP_DIGESTION, BENPORATH_ES_WITH_H3K27ME3, GOBP_GLAND_MORPHOGENESIS, GOBP_B_CELL_ACTIVATION, LFA1_Q6, GOBP_ALPHA_BETA_T_CELL_DIFFERENTIATION, GRAESSMANN_APOPTOSIS_BY_SERUM_DEPRIVATION_UP, GRAESSMANN_RESPONSE_TO_MC_AND_SERUM_DEPRIVATION_UP, GOBP_LYMPH_NODE_DEVELOPMENT, GOBP_MYELOID_LEUKOCYTE_DIFFERENTIATION, USF_C, GOBP_GLYCEROLIPID_METABOLIC_PROCESS, GOBP_CELL_ACTIVATION_INVOLVED_IN_IMMUNE_RESPONSE, GOBP_DIGESTIVE_SYSTEM_DEVELOPMENT

GO Biological Process (26): cell fate specification (GO:0001708), leukocyte homeostasis (GO:0001776), plasma cell differentiation (GO:0002317), regulation of transcription by RNA polymerase II (GO:0006357), transcription by RNA polymerase II (GO:0006366), triglyceride metabolic process (GO:0006641), gland morphogenesis (GO:0022612), cell differentiation (GO:0030154), macrophage differentiation (GO:0030225), odontogenesis of dentin-containing tooth (GO:0042475), CD4-positive, alpha-beta T cell differentiation (GO:0043367), positive regulation of transcription by RNA polymerase II (GO:0045944), saliva secretion (GO:0046541), lymph node development (GO:0048535), spleen development (GO:0048536), Peyer’s patch development (GO:0048541), post-embryonic digestive tract morphogenesis (GO:0048621), regulation of epithelial cell proliferation (GO:0050678), leukocyte migration (GO:0050900), regulation of DNA-templated transcription (GO:0006355), immune response (GO:0006955), post-embryonic development (GO:0009791), gene expression (GO:0010467), B cell differentiation (GO:0030183), mucosa-associated lymphoid tissue development (GO:0048537), digestive tract development (GO:0048565)

GO Molecular Function (4): RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978), DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), sequence-specific double-stranded DNA binding (GO:1990837), DNA binding (GO:0003677)

GO Cellular Component (2): chromatin (GO:0000785), nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular developmental process	2
immune system process	2
transcription by RNA polymerase II	2
DNA-templated transcription	2
regulation of transcription by RNA polymerase II	2
hematopoietic or lymphoid organ development	2
RNA polymerase II transcription regulatory region sequence-specific DNA binding	2
cell fate commitment	1
homeostasis of number of cells	1
mature B cell differentiation involved in immune response	1
regulation of DNA-templated transcription	1
acylglycerol metabolic process	1
animal organ morphogenesis	1
gland development	1
myeloid leukocyte differentiation	1
mononuclear cell differentiation	1
odontogenesis	1
CD4-positive, alpha-beta T cell activation	1
alpha-beta T cell differentiation	1
positive regulation of DNA-templated transcription	1
body fluid secretion	1
digestive system process	1
secretion by tissue	1
mucosa-associated lymphoid tissue development	1
post-embryonic animal morphogenesis	1
digestive tract morphogenesis	1
regulation of cell population proliferation	1
epithelial cell proliferation	1
cell migration	1
regulation of gene expression	1
regulation of RNA biosynthetic process	1
cis-regulatory region sequence-specific DNA binding	1
chromatin	1
DNA-binding transcription factor activity	1
double-stranded DNA binding	1
sequence-specific DNA binding	1
nucleic acid binding	1
chromosome	1
cellular anatomical structure	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

978 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
NKX2-3	MADCAM1	Q13477	750
NKX2-3	PTPN2	P17706	746
NKX2-3	DLG5	Q8TDM6	668
NKX2-3	NOD2	Q9HC29	658
NKX2-3	CARD9	Q9H257	566
NKX2-3	IRGM	A1A4Y4	541
NKX2-3	NKX6-3	A6NJ46	532
NKX2-3	ENTR1	Q96C92	491
NKX2-3	IL23R	Q5VWK5	479
NKX2-3	ATG16L1	Q676U5	479
NKX2-3	SLC9A4	Q6AI14	468
NKX2-3	IL18R1	Q13478	452
NKX2-3	GPSM1	Q86YR5	430
NKX2-3	HAND2	P61296	406
NKX2-3	TNFSF15	O95150	405

IntAct

4 interactions, top by confidence:

A	B	Type	Score
	NKX2-3	psi-mi:“MI:0915”(physical association)	0.370
GTF2A1L	NKX2-3	psi-mi:“MI:0915”(physical association)	0.370
NKX2-3	ZNF212	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (4): NKX2-3 (Affinity Capture-RNA), NKX2-3 (Affinity Capture-MS), NKX2-3 (Two-hybrid), NKX2-3 (Two-hybrid)

ESM2 similar proteins: A0A8V0YY16, A0JPN1, A7MB54, A8MTJ6, O35762, O42115, O57601, O88181, O95096, P09065, P23683, P28356, P31311, P31315, P32443, P39020, P42581, P42586, P43697, P48031, P49640, P50222, P50476, P52951, P52954, P52955, P78426, P81067, P81068, P97334, Q14549, Q14774, Q1KKY1, Q1XID0, Q2NKI2, Q2VL76, Q2VL80, Q4V5A3, Q5SQQ9, Q60554

Diamond homologs: A1YF16, A1YG93, A2RU54, A2T764, A6NCS4, A6NHT5, G5EE18, M0R6D8, O02786, O35767, O42230, O57601, O60479, O70218, P10181, P13297, P15857, P19601, P20009, P23410, P28360, P28361, P28362, P35548, P35993, P40764, P42580, P42581, P43687, P43688, P48031, P50219, P50223, P50574, P50575, P50576, P50577, P52953, P53547, P53770

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
NKX2-3	“up-regulates quantity by expression”	MADCAM1	“transcriptional regulation”

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	38
Likely benign	6
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

246 predictions. Top by Δscore:

Variant	Effect	Δscore
10:99533490:G:GG	donor_gain	1.0000
10:99534983:A:AG	acceptor_gain	1.0000
10:99534984:G:GG	acceptor_gain	1.0000
10:99534984:GAA:G	acceptor_gain	1.0000
10:99534984:GAAA:G	acceptor_gain	1.0000
10:99534979:CCGCA:C	acceptor_loss	0.9900
10:99534981:GCA:G	acceptor_loss	0.9900
10:99534982:CA:C	acceptor_loss	0.9900
10:99534983:A:AC	acceptor_loss	0.9900
10:99534984:G:GC	acceptor_loss	0.9900
10:99534984:GA:G	acceptor_gain	0.9900
10:99533486:CAAAG:C	donor_loss	0.9800
10:99533487:AAAG:A	donor_loss	0.9800
10:99533488:AA:A	donor_gain	0.9800
10:99533489:AGT:A	donor_loss	0.9800
10:99533490:G:C	donor_loss	0.9800
10:99533491:T:G	donor_loss	0.9800
10:99533492:GAG:G	donor_loss	0.9800
10:99533469:T:TA	donor_gain	0.9700
10:99533493:AGT:A	donor_loss	0.9700
10:99534246:G:T	donor_gain	0.9700
10:99534980:C:CA	acceptor_gain	0.9700
10:99533321:G:GT	donor_gain	0.9500
10:99534246:G:GT	donor_gain	0.9500
10:99533485:CCAAA:C	donor_gain	0.9200
10:99533467:GGTC:G	donor_gain	0.9100
10:99533468:GTCG:G	donor_gain	0.9100
10:99533470:C:CA	donor_gain	0.9100
10:99533486:CAAA:C	donor_gain	0.9100
10:99533487:AAA:A	donor_gain	0.9100

AlphaMissense

2355 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
10:99533165:T:C	F12L	1.000
10:99533166:T:C	F12S	1.000
10:99533166:T:G	F12C	1.000
10:99533167:C:A	F12L	1.000
10:99533167:C:G	F12L	1.000
10:99533172:T:A	V14D	1.000
10:99533181:T:A	I17N	1.000
10:99533181:T:C	I17T	1.000
10:99533181:T:G	I17S	1.000
10:99533184:T:C	L18S	1.000
10:99535084:T:A	V153D	1.000
10:99535087:T:A	L154H	1.000
10:99535089:T:A	F155I	1.000
10:99535089:T:C	F155L	1.000
10:99535089:T:G	F155V	1.000
10:99535090:T:C	F155S	1.000
10:99535090:T:G	F155C	1.000
10:99535091:C:A	F155L	1.000
10:99535091:C:G	F155L	1.000
10:99535103:G:C	Q159H	1.000
10:99535103:G:T	Q159H	1.000
10:99535105:T:A	V160D	1.000
10:99535114:T:A	L163Q	1.000
10:99535114:T:C	L163P	1.000
10:99535114:T:G	L163R	1.000
10:99535116:G:A	E164K	1.000
10:99535117:A:C	E164A	1.000
10:99535117:A:T	E164V	1.000
10:99535118:A:C	E164D	1.000
10:99535118:A:T	E164D	1.000

dbSNP variants (sampled 300 via entrez): RS1000984923 (10:99536176 C>T), RS1001118418 (10:99536234 G>C), RS1001565485 (10:99534217 C>T), RS1002275028 (10:99531465 T>C), RS1002300751 (10:99532905 C>A,T), RS1002443893 (10:99536915 C>T), RS1003397739 (10:99534291 G>A,T), RS1003575349 (10:99531665 G>A), RS1003868813 (10:99531948 G>C), RS1003911673 (10:99533573 G>A,C), RS1005584549 (10:99532263 C>T), RS1005899112 (10:99535894 G>T), RS1006077618 (10:99536996 C>A,G,T), RS1006534260 (10:99535571 C>A,G), RS1008084657 (10:99533962 G>A,C)

Disease associations

OMIM: gene MIM:606727 | disease phenotypes:

GenCC curated gene-disease

Disease	Classification	Inheritance
inflammatory bowel disease	Limited	Autosomal dominant

Mondo (1): inflammatory bowel disease (MONDO:0005265)

Orphanet (0):

HPO phenotypes

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

GWAS associations

35 associations (top):

Study	Trait	p-value
GCST000039_1	Crohn’s disease	4.000000e-10
GCST000042_4	Crohn’s disease	6.000000e-08
GCST000207_6	Crohn’s disease	3.000000e-16
GCST000623_5	Ulcerative colitis	2.000000e-06
GCST000624_8	Ulcerative colitis	1.000000e-08
GCST000879_57	Crohn’s disease	2.000000e-20
GCST001438_10	Crohn’s disease	5.000000e-07
GCST001713_31	Dental caries	6.000000e-06
GCST001725_7	Inflammatory bowel disease	1.000000e-54
GCST001765_9	Red blood cell traits	1.000000e-10
GCST002411_7	Colorectal cancer	5.000000e-11
GCST002919_10	Colorectal cancer	8.000000e-07
GCST003097_22	Pediatric autoimmune diseases	9.000000e-11
GCST003988_16	Hypothyroidism	1.000000e-10
GCST004131_22	Inflammatory bowel disease	2.000000e-34
GCST004132_16	Crohn’s disease	2.000000e-24
GCST004133_9	Ulcerative colitis	2.000000e-21
GCST004608_164	Granulocyte percentage of myeloid white cells	4.000000e-19
GCST004609_18	Monocyte percentage of white cells	2.000000e-25
GCST004625_183	Monocyte count	3.000000e-36
GCST004630_241	Mean corpuscular hemoglobin	3.000000e-16
GCST005529_50	Ankylosing spondylitis	5.000000e-14
GCST005529_57	Ankylosing spondylitis	2.000000e-14
GCST005537_194	Chronic inflammatory diseases (ankylosing spondylitis, Crohn’s disease, psoriasis, primary sclerosing cholangitis, ulcerative colitis) (pleiotropy)	6.000000e-51
GCST007552_4	Colorectal cancer	1.000000e-10
GCST007856_1	Colorectal cancer or advanced adenoma	4.000000e-06
GCST007856_18	Colorectal cancer or advanced adenoma	7.000000e-15
GCST008366_11	Leukocyte telomere length	2.000000e-07
GCST008366_19	Leukocyte telomere length	1.000000e-08
GCST008485_4	Crohn’s disease	8.000000e-08

EFO canonical traits (5, from GWAS)

EFO ID	Trait name
EFO:0004527	mean corpuscular hemoglobin
EFO:0007997	granulocyte percentage of myeloid white cells
EFO:0007989	monocyte percentage of leukocytes
EFO:0005091	monocyte count
EFO:0007874	gut microbiome measurement

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
D015212	Inflammatory Bowel Diseases	C06.405.205.731; C06.405.469.432

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
bisphenol A	decreases methylation	1
arsenite	increases methylation	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
zinc chromate	decreases expression, increases abundance	1
ferrous chloride	decreases expression	1
aflatoxin B2	decreases methylation	1
chromium hexavalent ion	decreases expression, increases abundance	1
CGP 52608	affects binding, increases reaction	1
entinostat	decreases expression	1
Air Pollutants	increases expression, increases abundance	1
Benzo(a)pyrene	affects methylation, decreases methylation, increases methylation	1
Valproic Acid	affects expression	1
Aflatoxin B1	decreases methylation	1
Palmitic Acid	increases expression	1
Particulate Matter	increases abundance, increases expression	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT00167882	PHASE4	COMPLETED	The Influence of 5-Aminosalicylates on Thiopurine Metabolite Levels
NCT00205062	PHASE4	TERMINATED	Positron Emission Tomography (PET)-Computed Tomography (CT) in Inflammatory Bowel Disease (IBD)
NCT00567593	PHASE4	COMPLETED	Gene Regulation by Thiazolidinediones
NCT00746395	PHASE4	COMPLETED	Randomized, Placebo-controlled Trial of Lubiprostone as a Preparation for Capsule Endoscopy
NCT01034358	PHASE4	COMPLETED	Immune Response to the Human Papillomavirus Vaccine in Young Women With Inflammatory Bowel Disease
NCT01056913	PHASE4	COMPLETED	NITI CAR27 (ColonRing) Compression Anastomosis in Colorectal Surgery
NCT01067547	PHASE4	COMPLETED	A Trial of Iron Replacement in Patients With Iron Deficiency.
NCT01341808	PHASE4	COMPLETED	Immunogenicity of Hepatitis A Vaccine in Inflammatory Bowel Disease (IBD) Patients
NCT01908283	PHASE4	COMPLETED	Induction of Immunity Against Streptococcus Pneumoniae in Adults With Inflammatory Bowel Disease
NCT01934088	PHASE4	COMPLETED	Satisfaction With Nurse Administered Propofol Sedation vs. Midazolam With Fentanyl Sedation for Endoscopy
NCT02162862	PHASE4	COMPLETED	Treating Disrupted Sleep in Individuals With Inflammatory Bowel Disease
NCT02248337	PHASE4	COMPLETED	Low Volume Colon Preparation for IBD
NCT02281799	PHASE4	WITHDRAWN	Thiopurine Induced Pancreatitis in IBD Patients
NCT02392286	PHASE4	TERMINATED	Corticosteroid Dosage for Crohn’s Disease Flare
NCT02437591	PHASE4	COMPLETED	Study to Evaluate the Pharmacokinetics of Fidaxomicin in Inflammatory Bowel Disease (IBD) Subjects With Clostridium Difficile Infection (CDI)
NCT02453776	PHASE4	COMPLETED	Precision Dosing of Infliximab Versus Conventional Dosing of Infliximab
NCT02461758	PHASE4	COMPLETED	Trial of High Dose vs. Standard Dose Influenza Vaccine in Inflammatory Bowel Disease Patients
NCT02566889	PHASE4	TERMINATED	An Efficacy and Safety Study of Infliximab Dose Escalation in Pediatric Participants With Inflammatory Bowel Disease
NCT02774057	PHASE4	UNKNOWN	Trial of Captafer® vs. Oral Iron Sulfate in the Treatment of Iron Deficiency Anemia in Patients With IBD
NCT02806206	PHASE4	UNKNOWN	Prucalopride Prior to Small Bowel Capsule Endoscopy
NCT02946203	PHASE4	COMPLETED	Comparison of VoLumen and Breeza Oral Contrast Agents in Pediatric Patients
NCT02994836	PHASE4	COMPLETED	GIS-SUSANTI-TNF-2015 (Anti-TNF Discontinuation )
NCT03220841	PHASE4	UNKNOWN	Stricture Definition and Treatment (STRIDENT) Drug Therapy Study
NCT03351972	PHASE4	COMPLETED	Differences in Preparation for Small Bowel Capsule Endoscopy
NCT03466983	PHASE4	COMPLETED	A Trial Comparing the Incidence of Hypophosphatemia in Relation to Treatment With Iron Isomaltoside and Ferric Carboxymaltose in Subjects With Iron Deficiency Anaemia Due to Inflammatory Bowel Disease
NCT03591770	PHASE4	TERMINATED	Shingrix Vaccine in Patients With Moderate to Severe Ulcerative Colitis on Tofacitinib
NCT03629379	PHASE4	COMPLETED	Response to Ustekinumab for Anti-tnf Induced Psoriasiform Skin Lesions
NCT03723447	PHASE4	COMPLETED	Intraoperative TAP Block With Bupivacaine/Dexamethasone Against Liposomal Bupivacaine (Exparel®)
NCT03798691	PHASE4	COMPLETED	Immunogenicity of Herpes Zoster Subunit Vaccine in Inflammatory Bowel Disease Patients Treated With Vedolizumab
NCT03860012	PHASE4	UNKNOWN	Folic Acid in Pediatric Inflammatory Bowel Disease
NCT03885713	PHASE4	COMPLETED	Identification of Predictive Biomarkers for Response to Biologic Therapies and Tofacitinib in Inflammatory Bowel Disease
NCT03917303	PHASE4	RECRUITING	Control Crohn Safe Trial
NCT04045782	PHASE4	COMPLETED	Evaluation of the Safety and Effectiveness of Switching From Humira® to Imraldi® in Flanders
NCT04304950	PHASE4	COMPLETED	Chronotherapy in Inflammatory Bowel Disease
NCT04626947	PHASE4	TERMINATED	Prevention of Recurrent Clostridium Difficile Infection (CDI) in Patients With Inflammatory Bowel Disease (IBD).
NCT04646187	PHASE4	ENROLLING_BY_INVITATION	De-escalation of Anti-TNF Therapy in Inflammatory Bowel Disease
NCT04835506	PHASE4	ACTIVE_NOT_RECRUITING	Proactive Infliximab Optimization Using a Pharmacokinetic Dashboard Versus Standard of Care in Patients With Inflammatory Bowel Disease: The OPTIMIZE Trial
NCT04982172	PHASE4	COMPLETED	Model-informed Dose De-escalation of Infliximab in Patients With Inflammatory Bowel Diseases
NCT05180175	PHASE4	COMPLETED	The Nordic IBD Treatment Strategy Trial
NCT05280405	PHASE4	UNKNOWN	Early Proactive Therapeutic Drug Monitoring of Infliximab in Children: EPIC Study