CDX1

Chr 5

caudal type homeobox 1

NCBI Gene: 1044ENSG00000113722UniProt: P47902

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. [provided by RefSeq, Jul 2008]

67
ClinVar variants
10
Pathogenic / LP
0.14
pLI score
0
Active trials
Clinical Summary— CDX1
⚡
Population Constraint (gnomAD)
Constrained for loss-of-function variants (OE-LoF 0.34) despite low pLI — interpret in context.
📋
ClinVar Variants
10 Pathogenic / Likely Pathogenic· 55 VUS of 67 total submissions

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
1.08LOEUF
pLI 0.143
Z-score 1.46
OE 0.34 (0.14–1.08)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
0.06Z-score
OE missense 0.98 (0.83–1.16)
99 obs / 100.8 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.34 (0.14–1.08)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.98 (0.83–1.16)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.0.85
0≤1.21.6
LoF obs/exp: 2 / 5.8Missense obs/exp: 99 / 100.8Syn Z: 0.77

ClinVar Variant Classifications

67 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic10
VUS55
Likely Benign2
10
Pathogenic
55
VUS
2
Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
10
0
10
Likely Pathogenic
0
0
0
0
0
VUS
0
54
1
0
55
Likely Benign
0
1
1
0
2
Benign
0
0
0
0
0
Total05512067

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

CDX1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Single-cell transcriptome profiling of post-treatment and treatment-naïve colorectal cancer: Insights into putative mechanisms of chemoresistance.
Puzanov GA et al.·Cancer Lett
2026Functional
RETRACTED: CDX1 Expression Induced by CagA-Expressing Helicobacter pylori Promotes Gastric Tumorigenesis.
Choi SI et al.·Mol Cancer Res
2019
N-Glycomic and Transcriptomic Changes Associated with CDX1 mRNA Expression in Colorectal Cancer Cell Lines.
Holst S et al.·Cells
2019
Cdx1 or Cdx2 expression activates E-cadherin-mediated cell-cell adhesion and compaction in human COLO 205 cells.
Keller MS et al.·Am J Physiol Gastrointest Liver Physiol
2004
Low CDX1 expression predicts a poor prognosis for hepatocellular carcinoma patients after hepatectomy.
Zheng H et al.·Surg Oncol
2016Cohort
Caudal genes in blood development and leukemia.
Lengerke C et al.·Ann N Y Acad Sci
2012Review
CDX1 confers intestinal phenotype on gastric epithelial cells via induction of stemness-associated reprogramming factors SALL4 and KLF5.
Fujii Y et al.·Proc Natl Acad Sci U S A
2012
Cdx1 and cdx2 expression during intestinal development.
Silberg DG et al.·Gastroenterology
2000
CDX1 is an important molecular mediator of Barrett's metaplasia.
Wong NA et al.·Proc Natl Acad Sci U S A
2005
Cdx1 and Cdx2 function as tumor suppressors.
Hryniuk A et al.·J Biol Chem
2014
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Myoepithelial Tumor of Soft Tissue With the Novel IRF2BP2::CDX1 Gene Fusion.
Naous R et al.·Cureus
2025🔓 Open Access
CDX1 and CDX2 suppress colon cancer stemness by inhibiting β-catenin-facilitated formation of Pol II-DSIF-PAF1C complex.
Aoki K et al.·Cell Death Dis
2025🔓 Open Access
CDX1 improves nicotine induced cardiac fibroblasts activation and cardiomyocyte hypertrophy by alleviating autophagic flux impairment through modulation of LAPTM4B.
Li YY et al.·Sci Rep
2025🔓 Open Access
Cdx1 and Gsc distinctly regulate the transcription of BMP4 target gene ventx3.2 by directly binding to the proximal promoter region in Xenopus gastrulae.
Goutam RS et al.·Mol Cells
2024🔓 Open Access
The Assessment of CDX1, IHH, SHH, GATA4, FOXA2, FOXF1 in Congenital Intra-Abdominal Adhesions.
Pope HF et al.·Acta Med Litu
2024
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

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External Resources

Links to major genomics databases and tools