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10 sources retrieved · Most recent: April 2026 · Index updated 14 days ago
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CDY1
chromodomain Y-linked 1
Chromosome Y · Yq11.23
NCBI Gene: 9085Ensembl: ENSG00000172288.8HGNC: HGNC:1809UniProt: Q9Y6F8
29PubMed Papers
16Diseases
0Drugs
0Pathogenic Variants
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
histone H3K27me3 reader activitynucleushistone H3K9me2/3 reader activitytranscription corepressor activityinfertilityazoospermiamale infertilityneoplasm
✦AI Summary

CDY1 is a Y-linked histone acetyltransferase with preference for histone H4 that functions as a transcriptional corepressor and histone reader with specificity for H3K27me3 and H3K9me2/3 marks 1. The gene plays a critical role in late-stage spermatogenesis, with CDY1 expression specifically associated with the presence of mature spermatids and spermatozoa rather than early germ cells 23. CDY1 deletions are implicated in male infertility: loss of both CDY1 copies combined with DAZ deletions significantly increases susceptibility to azoospermia (odds ratio 29.7) and severe oligozoospermia (odds ratio 26) 4. Complete deletion of CDY1a and CDY1b is present in all Sertoli cell-only syndrome patients examined, with no detectable CDY1 mRNA expression in affected individuals 5. Clinically, CDY1 expression assessment by qualitative RT-PCR serves as a predictive marker for sperm presence in testicular tissue, with 98.3% sensitivity 6. However, CDY1 deletions can be vertically transmitted via intracytoplasmic sperm injection, necessitating genetic counseling regarding infertility risk in future male offspring 4. Notably, CDY1 deletions are not universally essential for fertility, as documented cases of natural transmission of large AZFc deletions lacking CDY1 have occurred, suggesting compensatory mechanisms may exist in some individuals 1.

Sources cited
1
CDY1 deletions can be transmitted naturally and are not absolutely essential for fertility in exceptional individuals with compensatory mechanisms
PMID: 10956550
2
Loss of two DAZ and one CDY1 gene copies increases susceptibility to azoospermia (OR 29.7) and severe oligozoospermia (OR 26)
PMID: 26149076
3
CDY1 expression by qualitative RT-PCR has 98.3% sensitivity for predicting sperm cell presence in testicular tissue
PMID: 21474125
4
CDY1-minor expression correlates specifically with presence of mature spermatids/spermatozoa
PMID: 11163833
5
CDY1 is located with one copy in the DAZ cluster and another at its distal end; loss does not clearly worsen phenotype in DAZ-deleted patients
PMID: 11263480
6
CDY1a and CDY1b double deletions found in all SCOS patients with total germ cell depletion; no detectable CDY1 mRNA in affected individuals
PMID: 35358715
7
CDY1 transcripts correlate best with complete spermatogenesis; CDY1 is required in late stages while CDY2 is required in early stages of spermatogenesis
PMID: 14569460
Disease Associationsⓘ16
infertilityOpen Targets
0.01Suggestive
azoospermiaOpen Targets
0.01Suggestive
male infertilityOpen Targets
0.01Suggestive
neoplasmOpen Targets
0.01Suggestive
colon carcinomaOpen Targets
0.01Suggestive
Becker muscular dystrophyOpen Targets
0.00Suggestive
prostate cancerOpen Targets
0.00Suggestive
hepatocellular carcinomaOpen Targets
0.00Suggestive
pneumoniaOpen Targets
0.00Suggestive
small cell osteogenic sarcomaOpen Targets
0.00Suggestive
Abnormal sperm morphologyOpen Targets
0.00Suggestive
anemiaOpen Targets
0.00Suggestive
gastric cancerOpen Targets
0.00Suggestive
gliomaOpen Targets
0.00Suggestive
breast cancerOpen Targets
0.00Suggestive
cancerOpen Targets
0.00Suggestive
Pathogenic Variants
No pathogenic variants reported on ClinVar for this gene.
View on ClinVar ↗
Related Genes
H3C13Protein interaction95%H3C14Protein interaction94%H3-3AProtein interaction94%DAZ1Protein interaction92%RBMY1A1Protein interaction92%RBMY1CProtein interaction92%
Tissue Expression6 tissues
Liver
0%
Brain
0%
Lung
0%
Ovary
0%
Heart
0%
Bone Marrow
0%
Gene Interaction Network
Click a node to explore
CDY1H3C13H3C14H3-3ADAZ1RBMY1A1RBMY1C
PROTEIN STRUCTURE
Preparing viewer…
PDB6V41 · 1.60 Å · X-ray
View on RCSB ↗
RankingsWhere CDY1 stands among ~20K protein-coding genes
  • #12,119of 20,598
    Most Researched29
Genes detectedCDY1
Sources retrieved10 papers
Response time—
📄 Sources
10▼
1
The human Y chromosome genes BPY2, CDY1 and DAZ are not essential for sustained fertility.
PMID: 10956550
Mol Hum Reprod · 2000
1.00
2
Susceptibility of gr/gr rearrangements to azoospermia or oligozoospermia is dependent on DAZ and CDY1 gene copy deletions.
PMID: 26149076
J Assist Reprod Genet · 2015
0.90
3
CDY1 and BOULE transcripts assessed in the same biopsy as predictive markers for successful testicular sperm retrieval.
PMID: 21474125
Fertil Steril · 2011
0.80
4
Expression of CDY1 may identify complete spermatogenesis.
PMID: 11163833
Fertil Steril · 2001
0.70
5
CDY1 analysis in infertile patients with DAZ deletions.
PMID: 11263480
J Endocrinol Invest · 2001
0.60