CDX1

Summary

CDX1 (caudal type homeobox 1, HGNC:1805) is a protein-coding gene on chromosome 5q32, encoding Homeobox protein CDX-1 (P47902). Plays a role in transcriptional regulation.

This gene is a member of the caudal-related homeobox transcription factor gene family. The encoded DNA-binding protein regulates intestine-specific gene expression and enterocyte differentiation. It has been shown to induce expression of the intestinal alkaline phosphatase gene, and inhibit beta-catenin/T-cell factor transcriptional activity.

Source: NCBI Gene 1044 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 56 total
• Transcription factor: yes — 47 downstream targets (CollecTRI)
• MANE Select transcript: NM_001804

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:1805
Approved symbol	CDX1
Name	caudal type homeobox 1
Location	5q32
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000113722
Ensembl biotype	protein_coding
OMIM	600746
Entrez	1044

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000231656

RefSeq mRNA: 1 — MANE Select: NM_001804 NM_001804

CCDS: CCDS4304

Canonical transcript exons

ENST00000231656 — 3 exons

Exon	Start	End
ENSE00000767194	150182768	150182913
ENSE00000841174	150166778	150167321
ENSE00001663924	150183474	150184558

Expression profiles

Bgee: expression breadth ubiquitous, 124 present calls, max score 99.13.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 1.3899 / max 340.3490, expressed in 110 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
59412	1.3899	110

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
mucosa of transverse colon	UBERON:0004991	99.13	gold quality
rectum	UBERON:0001052	97.76	gold quality
ileal mucosa	UBERON:0000331	96.47	gold quality
colonic mucosa	UBERON:0000317	95.34	gold quality
mucosa of sigmoid colon	UBERON:0004993	95.08	gold quality
duodenum	UBERON:0002114	91.11	gold quality
small intestine Peyer’s patch	UBERON:0003454	89.92	gold quality
transverse colon	UBERON:0001157	89.35	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	89.08	gold quality
small intestine	UBERON:0002108	88.95	gold quality
jejunal mucosa	UBERON:0000399	88.71	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	88.43	gold quality
gluteal muscle	UBERON:0002000	87.51	gold quality
triceps brachii	UBERON:0001509	87.05	gold quality
type B pancreatic cell	CL:0000169	84.38	gold quality
olfactory bulb	UBERON:0002264	84.07	gold quality
diaphragm	UBERON:0001103	83.37	gold quality
intestine	UBERON:0000160	81.42	gold quality
jejunum	UBERON:0002115	80.59	gold quality
large intestine	UBERON:0000059	78.88	gold quality
colonic epithelium	UBERON:0000397	78.75	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	78.37	gold quality
colon	UBERON:0001155	78.15	gold quality
vermiform appendix	UBERON:0001154	77.96	gold quality
caecum	UBERON:0001153	77.71	gold quality
vastus lateralis	UBERON:0001379	77.31	gold quality
parotid gland	UBERON:0001831	77.01	gold quality
heart right ventricle	UBERON:0002080	76.57	gold quality
myocardium	UBERON:0002349	76.29	gold quality
quadriceps femoris	UBERON:0001377	75.81	gold quality

Single-cell (SCXA)

Detected in 6 experiment(s), a significant marker in 5.

Experiment	Marker?	Max mean expression
E-MTAB-8060	yes	244.43
E-MTAB-9388	yes	230.97
E-MTAB-10018	yes	122.22
E-MTAB-8410	yes	14.93
E-ANND-3	yes	7.06
E-GEOD-109979	no	50.66

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

47 targets.

Target	Regulation
ADA	Unknown
ALPI	Activation
ANXA5
APC
B3GALT5	Unknown
BCL2
CALB1
CCL25	Activation
CCND1	Repression
CDX1	Repression
CDX2	Unknown
CDX4
CEL
CLDN1
CLDN2	Activation
DLL1	Unknown
DSC2	Unknown
FOXA2	Unknown
GATA5	Unknown
GPA33	Unknown
HDC
HNF4A
HOXA9	Unknown
HOXB4	Activation
IAPP
INS
IRF2BP2	Unknown
KRT20	Unknown
MAFB	Repression
MUC2	Unknown

JASPAR motifs

Motif	Name	Family
MA0878.1	CDX1	HOX
MA0878.2	CDX1	HOX
MA0878.3	CDX1	HOX

JASPAR matrix evidence (PMIDs): PMID:18585359

Upstream regulators (CollecTRI, top): CDX1, CDX2, CTNNB1, HNF4A, HOXB7, LEF1, MAFB, MYBL1, NFKB, NR0B2, TCF7L2, THRA, TP53

miRNA regulators (miRDB)

35 targeting CDX1, 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-4283	100.00	66.42	2097
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-218-5P	99.93	72.22	2103
HSA-MIR-765	99.84	68.24	2442
HSA-MIR-11181-3P	99.75	66.38	2205
HSA-MIR-217-5P	99.49	69.93	1419
HSA-MIR-155-5P	99.35	70.16	1509
HSA-MIR-4311	99.31	70.47	3041
HSA-MIR-580-5P	99.28	70.94	1776
HSA-MIR-4721	99.26	66.05	818
HSA-MIR-361-3P	99.19	66.45	1381
HSA-MIR-4292	99.16	65.57	1767
HSA-MIR-6791-5P	99.16	65.92	1844
HSA-MIR-1253	99.12	67.08	1688
HSA-MIR-485-5P	99.10	64.78	1889
HSA-MIR-6884-5P	99.10	64.50	1987
HSA-MIR-1843	98.97	66.07	838
HSA-MIR-4802-5P	98.97	66.26	833
HSA-MIR-3194-3P	98.83	66.22	1167
HSA-MIR-6848-5P	98.81	65.49	1126
HSA-MIR-6846-5P	98.81	65.86	1121
HSA-MIR-4260	98.78	65.37	848
HSA-MIR-4635	98.74	67.63	1339
HSA-MIR-2467-3P	98.65	67.18	1969
HSA-MIR-1227-5P	98.65	65.32	1549
HSA-MIR-4736	97.96	65.89	1287
HSA-MIR-4446-3P	97.91	64.29	991
HSA-MIR-493-3P	97.50	66.44	731

Literature-anchored findings (GeneRIF, showing 40)

• Increased CDX1 mRNA expression is associated with chronic atrophic gastritis (PMID:11846061)
• CDX1 is downregulated after promoter methylation in colorectal tumor cell lines (PMID:12124393)
• these data show that Cdx1 exhibits a complex pattern during colorectal cancer progression, a high level of expression in polyps, and in one-third of the specimens, suggest that this gene may be a factor in the process toward malignant transformation (PMID:12970739)
• absence of CDX1 mRNA expression in 7 of 37 CRC cell lines and shown that all 7 cell lines have a methylated CDX1 promoter (PMID:14704280)
• Upstream sequences contain regulatory elements directing transgene expression specifically to intestinal epithelium. Two active chromatin regions in CDX1 gene may function as potential intestine-specific enhancers. (PMID:14715525)
• Cdx1 and Cdx2 inhibit colon cancer cell proliferation by blocking beta-catenin/TCF transcriptional activity (PMID:15215241)
• Cdx1 activates the IAP gene via a novel cis element, whereas Cdx2 inhibits the Cdx1 effects (PMID:15774940)
• Demethylation of the CDX1 promoter may be the key to the induction and maintenance of its expression and so of the Barrett’s metaplasia phenotype. (PMID:15894614)
• changes in CDX2 and CDX1 expression determined by methyl group deprivation may constitute one of the mechanisms sustaining the protective role attributed to folate in colon cancer (PMID:18187048)
• Cdx1 is not an oncogene in normal intestinal epithelium. (PMID:18231635)
• The ability of Cdx1 and c-myc to initiate the earliest stages of transdifferentiation of esophageal keratinocytes toward a cell fate characteristic of Barrett’s esophagus. (PMID:18953412)
• CDX1 enhanced the expression of PPARgamma gene, a master transcriptional regulator of intestinal differentiation, at the transcriptional level, via functional interaction with CCAAT/enhancer-binding protein alpha (C/EBPalpha). (PMID:19059241)
• KRT20 is directly regulated by CDX1, suggesting a role for CDX1 in maintaining differentiation in intestinal epithelial cells (PMID:19188603)
• Our data suggested an important role of CDX1 and CDX2 in the development of Barrett’s esophagus (PMID:19468668)
• RNA interference of CDX1 and CDX2 and chromatin immunoprecipitation in colon cancer cells revealed that MS4A12 transcript and protein expression is essentially dependent on the presence of endogenous CDX2. (PMID:19781065)
• Expression of CDX1 and CDX4 is not correlated with the pathogenesis and relapse of adult ALL. (PMID:21518475)
• CDX1 and CDX2 in cancer group was significantly higher than control group (PMID:21532856)
• The human ASBT promoter was activated transcriptionally by CDX1 and CDX2. (PMID:22016432)
• The epigenetic inactivation of CDX1 by promoter methylation, as well as the functional link of CDX1 promoter methylation to the inflammatory NF-kappaB signaling pathway, were investigated. (PMID:22749770)
• SALL4 and KLF5 were aberrantly expressed in the CDX1(+) intestinal metaplasia of the stomach. Sustained expression of CDX1 gave rise to the induction of early intestinal-stemness markers, followed by the expression of intestinal-differentiation markers. (PMID:23112162)
• The homeotic transcription factor CDX1 is expressed in the intestinal epithelium at all stages of development. Review. (PMID:23127929)
• analysis of an IRF2BP2-CDX1 fusion gene brought about by translocation t(1;5)(q42;q32) in mesenchymal chondrosarcoma (PMID:23185413)
• The findings represented the relation between CDX1 mutations and CDX1 genotype. Furthermore, it was suggested that the downregulation of CDX1 might be related to the development of Anorectal malformations . (PMID:23329892)
• Results showed an anti-growth effect of CDX1 and identified its miRNA regulatory mechanism in gastric cancer. (PMID:23353818)
• The differential regulation of the gene expression of CDX1, CDX2 and SOX2 in patients with gastric cancer affects not only the tumour but also the non-neoplastic tumour-distant mucosa. (PMID:23613102)
• Oxidative stress regulates CDX1 expression in T84 colorectal cancer cells. (PMID:23618814)
• Data indicate that autophagy is activated though the Cdx1-Bcl-2-LC3 pathway. (PMID:23624503)
• Certain SNPs of Cdx1 and Cdx2 and their interactions with other risk factors are associated with Barrett’s esophagus (BE) and may contribute to human susceptibility to BE. (PMID:23918153)
• CDX1 restricts the invasion of HTR-8/SVneo trophoblast cells by inhibiting MMP-9 expression independently of the PI3K/AKT pathway. (PMID:24836459)
• miR-215 is a link between CDX1 expression and BMI1 repression that governs differentiation in colorectal cancer (PMID:25775580)
• Data indicate an association between highly fucosylated glycans and caudal type homeobox 1 (CDX1) and/or villin mRNA expression that both correlate with cell differentiation. (PMID:26537799)
• Changes in CDX1/CDX2 mRNA expression in gastric mucosa following H. pylori eradication showed only insignificant results (PMID:26841784)
• Downregulation of CDX1 is associated with recurrence in hepatocellular carcinoma. (PMID:27566019)
• Results identified CDX1 as cis methylation quantitative trait loci in allergic rhinitis. (PMID:28149331)
• XIST is down-regulated in breast cancer and suppresses breast cancer cell growth, migration, and invasion via the miR-155/CDX1 axis. caudal-type homeobox 1 (CDX1) was identified as a direct target of miR-155 and miR-155/CDX1 rescued the effects of XIST in breast cancer cells. (PMID:29550489)
• High CDX1 expression is associated with esophageal adenocarcinoma. (PMID:30486614)
• Low CDX1 expression is correlated with Gastric Adenocarcinoma. (PMID:30685841)
• These data highlight a possible role of CDX1 in altering the N-glycosylation of colorectal cancer cells, which is a hallmark of tumor development. (PMID:30909444)
• LncRNA FOXD2-AS1 accelerates the progression of cervical cancer via downregulating CDX1. (PMID:31841177)
• The effect of miR-372-5p regulation on CDX1 and CDX2 in the gastric cancer cell line. (PMID:36848481)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Cdx1	ENSMUSG00000024619
rattus_norvegicus	Cdx1	ENSRNOG00000060334

Paralogs (2): CDX4 (ENSG00000131264), CDX2 (ENSG00000165556)

Protein

Protein identifiers

Homeobox protein CDX-1 — P47902 (reviewed: P47902)

Alternative names: Caudal-type homeobox protein 1

All UniProt accessions (1): P47902

UniProt curated annotations — full annotation on UniProt →

Function. Plays a role in transcriptional regulation. Involved in activated KRAS-mediated transcriptional activation of PRKD1 in colorectal cancer (CRC) cells. Binds to the PRKD1 promoter in colorectal cancer (CRC) cells. Could play a role in the terminal differentiation of the intestine. Binds preferentially to methylated DNA.

Subcellular location. Nucleus.

Tissue specificity. Intestinal epithelium.

Similarity. Belongs to the Caudal homeobox family.

Isoforms (2)

UniProt ID	Names	Canonical?
P47902-1	1	yes
P47902-2	2

RefSeq proteins (1): NP_001795* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000047	HTH_motif	Conserved_site
IPR001356	HD	Domain
IPR006820	Caudal_activation_dom	Domain
IPR009057	Homeodomain-like_sf	Homologous_superfamily
IPR017970	Homeobox_CS	Conserved_site
IPR020479	HD_metazoa	Domain
IPR047152	Caudal_homeobox	Family

Pfam: PF00046, PF04731

UniProt features (20 total): compositionally biased region 6, region of interest 4, helix 3, chain 1, DNA-binding region 1, splice variant 1, sequence variant 1, sequence conflict 1, strand 1, turn 1

Structure

Experimental structures (PDB)

2 structures.

PDB	Method	Resolution (Å)
7Q3O	X-RAY DIFFRACTION	2.78
5LUX	X-RAY DIFFRACTION	3.23

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P47902-F1	69.02	0.25

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 113 (showing top): GOBP_EMBRYO_DEVELOPMENT_ENDING_IN_BIRTH_OR_EGG_HATCHING, GOBP_EPITHELIUM_DEVELOPMENT, BENPORATH_ES_WITH_H3K27ME3, GOBP_AXIS_SPECIFICATION, PAX4_01, GOBP_SKELETAL_SYSTEM_DEVELOPMENT, SP3_Q3, GGGTGGRR_PAX4_03, CAGCTG_AP4_Q5, COUP_01, GOBP_DIGESTIVE_SYSTEM_DEVELOPMENT, TCF4_Q5, GOBP_ANIMAL_ORGAN_MORPHOGENESIS, GOBP_BONE_DEVELOPMENT, GOBP_ANTERIOR_POSTERIOR_PATTERN_SPECIFICATION

GO Biological Process (13): regulation of transcription by RNA polymerase II (GO:0006357), embryonic pattern specification (GO:0009880), animal organ morphogenesis (GO:0009887), anterior/posterior axis specification (GO:0009948), regulation of somitogenesis (GO:0014807), cell differentiation (GO:0030154), positive regulation of transcription by RNA polymerase II (GO:0045944), digestive tract development (GO:0048565), bone morphogenesis (GO:0060349), regulation of DNA-templated transcription (GO:0006355), multicellular organism development (GO:0007275), pattern specification process (GO:0007389), anterior/posterior pattern specification (GO:0009952)

GO Molecular Function (10): transcription cis-regulatory region binding (GO:0000976), RNA polymerase II transcription regulatory region sequence-specific DNA binding (GO:0000977), RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978), DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), DNA-binding transcription activator activity, RNA polymerase II-specific (GO:0001228), DNA-binding transcription factor activity (GO:0003700), methyl-CpG binding (GO:0008327), sequence-specific double-stranded DNA binding (GO:1990837), DNA binding (GO:0003677), protein binding (GO:0005515)

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

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
RNA polymerase II transcription regulatory region sequence-specific DNA binding	3
regulation of DNA-templated transcription	2
transcription by RNA polymerase II	2
regulation of transcription by RNA polymerase II	2
multicellular organismal process	2
transcription cis-regulatory region binding	2
sequence-specific DNA binding	2
pattern specification process	1
embryo development	1
anatomical structure morphogenesis	1
animal organ development	1
axis specification	1
anterior/posterior pattern specification	1
somitogenesis	1
regulation of anatomical structure morphogenesis	1
regulation of multicellular organismal process	1
cellular developmental process	1
positive regulation of DNA-templated transcription	1
tube development	1
digestive system development	1
animal organ morphogenesis	1
skeletal system morphogenesis	1
bone development	1
DNA-templated transcription	1
regulation of gene expression	1
regulation of RNA biosynthetic process	1
anatomical structure development	1
multicellular organism development	1
regionalization	1
transcription regulatory region nucleic acid binding	1
sequence-specific double-stranded DNA binding	1
cis-regulatory region sequence-specific DNA binding	1
chromatin	1
DNA-binding transcription factor activity	1
DNA-binding transcription factor activity, RNA polymerase II-specific	1
DNA-binding transcription activator activity	1
positive regulation of transcription by RNA polymerase II	1
transcription regulator activity	1
nucleotide binding	1
double-stranded DNA binding	1

Protein interactions and networks

STRING

1366 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CDX1	TCOF1	Q13428	669
CDX1	ANXA6	P08133	639
CDX1	FOXA2	Q9Y261	624
CDX1	HNF1A	P20823	609
CDX1	CLDN2	P57739	599
CDX1	LEF1	Q9UJU2	599
CDX1	NDST1	P52848	588
CDX1	CLDN3	O15551	563
CDX1	SLC26A2	P50443	543
CDX1	TFF3	Q07654	527
CDX1	PDGFRB	P09619	515
CDX1	RPS14	P06366	513
CDX1	CSF1R	P07333	500
CDX1	CTNNB1	P35222	478
CDX1	AXIN2	Q9Y2T1	471

IntAct

12 interactions, top by confidence:

A	B	Type	Score
CEBPA	CDX1	psi-mi:“MI:0915”(physical association)	0.580
CDX1	CEBPA	psi-mi:“MI:0915”(physical association)	0.580
CDX1	ZMPSTE24	psi-mi:“MI:0915”(physical association)	0.400
CDX1	DDX42	psi-mi:“MI:0915”(physical association)	0.400
CDX1	TBP	psi-mi:“MI:0915”(physical association)	0.400
ECE1	CDX1	psi-mi:“MI:0915”(physical association)	0.370
CDX1	ZNF724	psi-mi:“MI:0914”(association)	0.350
CDX1	IPO7	psi-mi:“MI:0914”(association)	0.350

BioGRID (120): CEBPA (Reconstituted Complex), CEBPA (Two-hybrid), CDX1 (Affinity Capture-Western), CABIN1 (Affinity Capture-MS), HIRA (Affinity Capture-MS), DHX29 (Affinity Capture-MS), TUBA8 (Affinity Capture-MS), UBN2 (Affinity Capture-MS), ZCCHC6 (Affinity Capture-MS), ZNF724P (Affinity Capture-MS), KBTBD7 (Affinity Capture-MS), PUM2 (Affinity Capture-MS), KBTBD6 (Affinity Capture-MS), ZNF107 (Affinity Capture-MS), CDK12 (Affinity Capture-MS)

ESM2 similar proteins: A1YER7, A1YF08, A1YFD8, A1YFY3, A1YG01, A1YG85, A2D4P8, A2D4R4, A2D5I1, A2D649, A2T6H5, A2T6X6, A2T6Z0, A2T748, A2T756, A2T7H5, A2T7J2, P06798, P09016, P09017, P09023, P09024, P10284, P10628, P13378, P14653, P17277, P17483, P17509, P18111, P18864, P23463, P23813, P31259, P31275, P31276, P31277, P31310, P47902, P50207

Diamond homologs: A1YFA5, A2D5K9, A2D5Y4, A2T7F3, A2T7H5, A8XSQ8, O13074, O14627, O42504, P02830, P02832, P02833, P04476, P06798, P07548, P09013, P09014, P09017, P09019, P09021, P09023, P09024, P09067, P09070, P09071, P09077, P09079, P09080, P09085, P09092, P09629, P09630, P10038, P10178, P10284, P10629, P13545, P14838, P14839, P14840

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
CDX1	“up-regulates quantity by expression”	VIL1	“transcriptional regulation”

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	54
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

520 predictions. Top by Δscore:

Variant	Effect	Δscore
5:150167319:GCG:G	donor_gain	1.0000
5:150182758:T:A	acceptor_gain	1.0000
5:150182764:TCA:T	acceptor_loss	1.0000
5:150182765:CAGG:C	acceptor_loss	1.0000
5:150182766:AG:A	acceptor_gain	1.0000
5:150182767:GG:G	acceptor_gain	1.0000
5:150182767:GGTA:G	acceptor_gain	1.0000
5:150182767:GGTAA:G	acceptor_gain	1.0000
5:150182911:CAGGT:C	donor_loss	1.0000
5:150182913:GG:G	donor_loss	1.0000
5:150182914:G:A	donor_loss	1.0000
5:150182915:T:A	donor_loss	1.0000
5:150183472:A:AT	acceptor_loss	1.0000
5:150167322:G:GG	donor_gain	0.9900
5:150167323:TAA:T	donor_loss	0.9900
5:150182748:C:CA	acceptor_gain	0.9900
5:150182766:A:AG	acceptor_gain	0.9900
5:150182767:G:GA	acceptor_gain	0.9900
5:150182767:GGT:G	acceptor_gain	0.9900
5:150182909:GGCAG:G	donor_gain	0.9900
5:150182910:GCAG:G	donor_gain	0.9900
5:150182910:GCAGG:G	donor_gain	0.9900
5:150182911:C:T	donor_gain	0.9900
5:150182914:G:GG	donor_gain	0.9900
5:150183464:A:AG	acceptor_gain	0.9900
5:150183465:A:G	acceptor_gain	0.9900
5:150183469:CACAG:C	acceptor_gain	0.9900
5:150183470:ACAG:A	acceptor_gain	0.9900
5:150183470:ACAGG:A	acceptor_gain	0.9900
5:150183471:C:G	acceptor_gain	0.9900

AlphaMissense

1681 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
5:150182803:T:C	Y161H	1.000
5:150182828:T:A	L169Q	1.000
5:150182828:T:C	L169P	1.000
5:150182839:T:A	F173I	1.000
5:150182839:T:C	F173L	1.000
5:150182840:T:C	F173S	1.000
5:150182840:T:G	F173C	1.000
5:150182841:T:A	F173L	1.000
5:150182841:T:G	F173L	1.000
5:150182854:T:C	Y178H	1.000
5:150182872:A:G	K184E	1.000
5:150182874:A:C	K184N	1.000
5:150182874:A:T	K184N	1.000
5:150182882:T:C	L187P	1.000
5:150182885:C:A	A188D	1.000
5:150182900:T:C	L193P	1.000
5:150183477:A:G	K199E	1.000
5:150183479:G:C	K199N	1.000
5:150183479:G:T	K199N	1.000
5:150183481:T:A	I200N	1.000
5:150183481:T:C	I200T	1.000
5:150183481:T:G	I200S	1.000
5:150183483:T:A	W201R	1.000
5:150183483:T:C	W201R	1.000
5:150183485:G:C	W201C	1.000
5:150183485:G:T	W201C	1.000
5:150183486:T:A	F202I	1.000
5:150183486:T:C	F202L	1.000
5:150183486:T:G	F202V	1.000
5:150183487:T:C	F202S	1.000

dbSNP variants (sampled 300 via entrez): RS1000150114 (5:150178784 G>A), RS1000361667 (5:150171054 T>A), RS1000440457 (5:150181387 C>T), RS1000469446 (5:150169377 G>A), RS1000471555 (5:150181713 T>A), RS1000619487 (5:150169360 C>G,T), RS1000692932 (5:150169606 C>T), RS1000712055 (5:150169524 C>G,T), RS1000816607 (5:150165680 A>G,T), RS1000901033 (5:150175807 C>A), RS1001029329 (5:150181294 G>A), RS1001269773 (5:150175475 G>A), RS1001288935 (5:150180526 G>T), RS1001567346 (5:150181838 G>T), RS1001598479 (5:150182102 C>A)

Disease associations

OMIM: gene MIM:600746 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

4 associations (top):

Study	Trait	p-value
GCST010396_208	Gut microbiota (bacterial taxa, hurdle binary method)	4.000000e-06
GCST012202_2	Distal/Left-sided colorectal cancer	5.000000e-09
GCST012204_2	Rectal cancer	2.000000e-06
GCST012205_3	Distal colorectal cancer	5.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0007874	gut microbiome measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

16 total (human), top 16 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, increases methylation	2
pirinixic acid	affects binding, decreases expression, increases activity	1
bisphenol A	decreases methylation	1
aflatoxin B2	increases methylation	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	decreases reaction, increases expression, increases reaction	1
Chir 99021	increases expression, increases reaction, decreases reaction	1
(+)-JQ1 compound	decreases expression	1
Resveratrol	decreases expression	1
Decitabine	increases expression	1
Arsenic Trioxide	decreases expression	1
Benzo(a)pyrene	decreases methylation	1
Folic Acid	increases expression	1
Dronabinol	decreases expression	1
Tretinoin	decreases reaction, increases expression, increases reaction	1
Triclosan	increases expression	1
8-Bromo Cyclic Adenosine Monophosphate	decreases expression	1

Clinical trials (associated diseases)

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