CDO1

Chr 5

cysteine dioxygenase type 1

Also known as: CDO-I

NCBI Gene: 1036ENSG00000129596UniProt: Q16878

Enables cysteine dioxygenase activity; ferrous iron binding activity; and zinc ion binding activity. Predicted to be involved in L-cysteine catabolic process. Predicted to be located in cytosol. [provided by Alliance of Genome Resources, Jul 2025]

54
ClinVar variants
24
Pathogenic / LP
0.01
pLI score
2
Active trials
Clinical Summary— CDO1
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.01) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
24 Pathogenic / Likely Pathogenic· 27 VUS of 54 total submissions
💊
Clinical Trials
2 active or recruiting trials — potential therapeutic options may be available

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.
0.93LOEUF
pLI 0.010
Z-score 1.74
OE 0.44 (0.23–0.93)
Tolerant

Typical tolerance to LoF variation

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.
0.19Z-score
OE missense 0.95 (0.81–1.12)
104 obs / 109.6 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.0.44 (0.23–0.93)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.95 (0.81–1.12)
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.0.74
0≤1.21.6
LoF obs/exp: 5 / 11.3Missense obs/exp: 104 / 109.6Syn Z: 1.28

ClinVar Variant Classifications

54 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic23
Likely Pathogenic1
VUS27
Likely Benign3
23
Pathogenic
1
Likely Pathogenic
27
VUS
3
Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
23
0
23
Likely Pathogenic
0
0
1
0
1
VUS
0
25
2
0
27
Likely Benign
0
1
2
0
3
Benign
0
0
0
0
0
Total02628054

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

View in ClinVar →

Protein Context — Lollipop Plot

CDO1 · protein map & ClinVar variants

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

Gene2Phenotype Curations

CDO1-related neurodevelopmental disorder

limited
ADUndeterminedAltered Gene Product Structure
Dev. Disorders
G2P ↗
missense variant

Gene2Phenotype curations · DECIPHER consortium patient cohort (public variants) · deciphergenomics.org

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
TRIM47-CDO1 axis dictates hepatocellular carcinoma progression by modulating ferroptotic cell death through the ubiquitin‒proteasome system.
Zhang J et al.·Free Radic Biol Med
2024
Targeted demethylation of the CDO1 promoter based on CRISPR system inhibits the malignant potential of breast cancer cells.
Yang J et al.·Clin Transl Med
2023
Promoter DNA methylation of CDO1 gene and its clinical significance in esophageal squamous cell carcinoma.
Ushiku H et al.·Dis Esophagus
2017
Diagnostic Value of CDO1 Promoter Methylation in Lung Cancer via Liquid Biopsy: A Systematic Review and Meta-Analysis.
Yan Y et al.·Front Biosci (Landmark Ed)
2025Meta-analysis
Biomarkers and potential function analysis of triple-negative breast cancer screening based on bioinformatics.
Chen X et al.·Cancer Biomark
2025
Differential Prognostic Relevance of Promoter DNA Methylation of CDO1 and HOPX in Primary Breast Cancer.
Tanaka Y et al.·Anticancer Res
2019
Integration of epigenomic and transcriptomic profiling uncovers EZH2 target genes linked to cysteine metabolism in hepatocellular carcinoma.
Lee J et al.·Cell Death Dis
2024
Pan-cancer methylation analysis of circulating cell-free DNA.
Dong W et al.·Cancer Genet
2025
Methylated promoter DNA of CDO1 gene and preoperative serum CA19-9 are prognostic biomarkers in primary extrahepatic cholangiocarcinoma.
Nakamoto S et al.·PLoS One
2018
Epigenetic Status of CDO1 Gene May Reflect Chemosensitivity in Colon Cancer with Postoperative Adjuvant Chemotherapy.
Yokoi K et al.·Ann Surg Oncol
2019
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov
Epithelial Ovarian CancerCirculating Tumor DNADNA Methylation

ctDNA Methylation for Epithelial Ovarian Cancer

RECRUITING
NCT05801263Lei LiStarted 2023-03-24
CDO1 and HOXA9 methylation assay
Epithelial Ovarian CancerCirculating Tumor DNADNA Methylation

ctDNA Methylation for Detecting Ovarian Cancer

RECRUITING
NCT05801276Lei LiStarted 2023-03-24
Methylation assay

External Resources

Links to major genomics databases and tools