CDY2B

Summary

CDY2B (chromodomain Y-linked 2B, HGNC:23921) is a protein-coding gene on chromosome Yq11.222, encoding Testis-specific chromodomain protein Y 2 (Q9Y6F7). May have histone acetyltransferase activity.

This intronless gene encodes a protein containing a chromodomain and a histone acetyltransferase catalytic domain. Chromodomain proteins are components of heterochromatin-like complexes and can act as gene repressors. This protein is localized to the nucleus of late spermatids where histone hyperacetylation takes place. Histone hyperacetylation is thought to facilitate the transition in which protamines replace histones as the major DNA-packaging protein. Two nearly identical copies of this gene are found in a palindromic region on chromosome Y; this record represents the centromeric copy. Chromosome Y also contains a pair of closely related genes in another more telomeric palindrome as well as several related pseudogenes.

Source: NCBI Gene 203611 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 1 total
• MANE Select transcript: NM_001001722

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23921
Approved symbol	CDY2B
Name	chromodomain Y-linked 2B
Location	Yq11.222
Locus type	gene with protein product
Status	Approved
Aliases	CDY
Ensembl gene	ENSG00000129873
Ensembl biotype	protein_coding
Entrez	203611

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000382867

RefSeq mRNA: 1 — MANE Select: NM_001001722 NM_001001722

CCDS: CCDS35473

Canonical transcript exons

ENST00000382867 — 1 exons

Exon	Start	End
ENSE00002314376	17878260	17880220

Expression profiles

Bgee: expression breadth tissue_specific, 3 present calls, max score 37.20.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
colonic epithelium	UBERON:0000397	37.20	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
bone marrow cell	CL:0002092	36.16	gold quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
skeletal muscle tissue	UBERON:0001134	33.38	gold quality
hindlimb stylopod muscle	UBERON:0004252	32.15	gold quality
bone marrow	UBERON:0002371	31.74	gold quality
muscle tissue	UBERON:0002385	31.06	gold quality
sural nerve	UBERON:0015488	30.93	gold quality
stromal cell of endometrium	CL:0002255	29.87	gold quality
prefrontal cortex	UBERON:0000451	29.04	gold quality
liver	UBERON:0002107	28.76	gold quality
urinary bladder	UBERON:0001255	28.40	gold quality
duodenum	UBERON:0002114	28.14	gold quality
monocyte	CL:0000576	27.70	gold quality
leukocyte	CL:0000738	27.69	gold quality
lymph node	UBERON:0000029	27.57	gold quality
tonsil	UBERON:0002372	27.05	gold quality
islet of Langerhans	UBERON:0000006	26.55	gold quality
vermiform appendix	UBERON:0001154	26.42	gold quality
right coronary artery	UBERON:0001625	26.39	gold quality
blood	UBERON:0000178	26.19	gold quality
gall bladder	UBERON:0002110	25.98	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	25.89	gold quality
placenta	UBERON:0001987	25.81	gold quality
muscle of leg	UBERON:0001383	25.12	gold quality
primary visual cortex	UBERON:0002436	24.61	gold quality
uterine cervix	UBERON:0000002	24.32	gold quality
kidney	UBERON:0002113	24.20	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.09

Regulation

Is transcription factor: no

Cross-species orthologs

12 orthologs

Organism	Symbol	Gene ID
danio_rerio	cdyl	ENSDARG00000038985
mus_musculus	Cdyl	ENSMUSG00000059288
rattus_norvegicus	AABR07039112.1	ENSRNOG00000022855
drosophila_melanogaster	CG14787	FBGN0027793
drosophila_melanogaster	CG8778	FBGN0033761
drosophila_melanogaster	Dci	FBGN0035169
drosophila_melanogaster	HIPP1	FBGN0037027
drosophila_melanogaster	Srlp	FBGN0038049
drosophila_melanogaster	CG5611	FBGN0039531
caenorhabditis_elegans		WBGENE00001152
caenorhabditis_elegans		WBGENE00001154
caenorhabditis_elegans		WBGENE00007130

Paralogs (13): ECHDC1 (ENSG00000093144), ECH1 (ENSG00000104823), ECHDC2 (ENSG00000121310), ECHS1 (ENSG00000127884), ECHDC3 (ENSG00000134463), AUH (ENSG00000148090), CDYL (ENSG00000153046), CDYL2 (ENSG00000166446), ECI1 (ENSG00000167969), CDY1 (ENSG00000172288), CDY1B (ENSG00000172352), CDY2A (ENSG00000182415), HIBCH (ENSG00000198130)

Protein

Protein identifiers

Testis-specific chromodomain protein Y 2 — Q9Y6F7 (reviewed: Q9Y6F7)

All UniProt accessions (1): Q9Y6F7

UniProt curated annotations — full annotation on UniProt →

Function. May have histone acetyltransferase activity.

Subcellular location. Nucleus.

Tissue specificity. Testis specific.

RefSeq proteins (1): NP_001001722* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000953	Chromo/chromo_shadow_dom	Domain
IPR001753	Enoyl-CoA_hydra/iso	Domain
IPR014748	Enoyl-CoA_hydra_C	Homologous_superfamily
IPR016197	Chromo-like_dom_sf	Homologous_superfamily
IPR017984	Chromo_dom_subgr	Domain
IPR023779	Chromodomain_CS	Conserved_site
IPR023780	Chromo_domain	Domain
IPR029045	ClpP/crotonase-like_dom_sf	Homologous_superfamily
IPR051053	ECH/Chromodomain_protein	Family

Pfam: PF00378, PF00385

Catalyzed reactions (Rhea), 1 shown:

• L-lysyl-[protein] + acetyl-CoA = N(6)-acetyl-L-lysyl-[protein] + CoA + H(+) (RHEA:45948)

UniProt features (25 total): helix 12, strand 9, chain 1, domain 1, region of interest 1, compositionally biased region 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
2FW2	X-RAY DIFFRACTION	2.2

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9Y6F7-F1	71.50	0.50

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 33 (showing top): GOBP_MALE_GAMETE_GENERATION, GOBP_NEGATIVE_REGULATION_OF_PROTEIN_METABOLIC_PROCESS, GOBP_DEVELOPMENTAL_PROCESS_INVOLVED_IN_REPRODUCTION, GOBP_PROTEIN_ACYLATION, GOBP_NEGATIVE_REGULATION_OF_PROTEIN_MODIFICATION_PROCESS, GOBP_REGULATION_OF_PROTEIN_MODIFICATION_PROCESS, GOMF_ACETYLTRANSFERASE_ACTIVITY, GOMF_ACYLTRANSFERASE_ACTIVITY, GOMF_N_ACYLTRANSFERASE_ACTIVITY, GOMF_TRANSCRIPTION_COREPRESSOR_ACTIVITY, GOMF_N_ACETYLTRANSFERASE_ACTIVITY, GOBP_REGULATION_OF_PROTEIN_METABOLIC_PROCESS, chrYq11, GOBP_NEGATIVE_REGULATION_OF_NUCLEOBASE_CONTAINING_COMPOUND_METABOLIC_PROCESS, GOMF_TRANSCRIPTION_COREGULATOR_ACTIVITY

GO Biological Process (3): spermatogenesis (GO:0007283), chromatin remodeling (GO:0006338), negative regulation of DNA-templated transcription (GO:0045892)

GO Molecular Function (5): transcription corepressor activity (GO:0003714), protein-lysine-acetyltransferase activity (GO:0061733), histone acetyltransferase activity (GO:0004402), transferase activity (GO:0016740), acyltransferase activity (GO:0016746)

GO Cellular Component (1): nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
developmental process involved in reproduction	1
male gamete generation	1
chromatin organization	1
DNA-templated transcription	1
regulation of DNA-templated transcription	1
negative regulation of RNA biosynthetic process	1
transcription coregulator activity	1
negative regulation of DNA-templated transcription	1
protein N-acetyltransferase activity	1
protein-lysine-acetyltransferase activity	1
histone modifying activity	1
catalytic activity	1
transferase activity	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

672 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CDY2B	BPY2	O14599	948
CDY2B	DAZ1	Q9NQZ3	943
CDY2B	VCY	O14598	933
CDY2B	DAZ2	Q13117	894
CDY2B	PRY	O14603	883
CDY2B	E7ERQ6	E7ERQ6	849
CDY2B	RBMY1A1	P0DJD3	769
CDY2B	HSFY1	Q96LI6	761
CDY2B	TSPY1	P09002	720
CDY2B	USP9Y	O00507	663
CDY2B	DDX3Y	O15523	655
CDY2B	EIF1AY	O14602	601
CDY2B	UTY	O14607	593
CDY2B	ZFY	P08048	591
CDY2B	KDM5D	Q9BY66	590

IntAct

2 interactions, top by confidence:

A	B	Type	Score
CDY2A	SMPD2	psi-mi:“MI:0914”(association)	0.350
AFG2B	MMP24OS	psi-mi:“MI:0914”(association)	0.350

BioGRID (25): MYCBP (Affinity Capture-MS), SMPD2 (Affinity Capture-MS), PRSS1 (Affinity Capture-MS), CDY2A (Affinity Capture-MS), SPIN1 (Affinity Capture-MS), CHCHD2 (Affinity Capture-MS), CDY2A (Affinity Capture-MS), HIST1H2AE (Affinity Capture-MS), WIZ (Affinity Capture-MS), ZNF644 (Affinity Capture-MS), ATF7IP (Affinity Capture-MS), ZNF644 (Affinity Capture-MS), SPIN3 (Affinity Capture-MS), CLTCL1 (Affinity Capture-MS), CDYL (Affinity Capture-MS)

ESM2 similar proteins: A0A0B7P3V8, A4FUB7, A4H7G5, A4HVU6, A6NKG5, B4NSS9, B6EU02, F4I1N8, H2KZW3, O10318, O13329, P04586, P0C2J7, P18475, P34601, P47024, Q01577, Q05101, Q09178, Q09293, Q1L6Q1, Q3S4A7, Q4DCH3, Q4QFY1, Q4R6I1, Q52QI2, Q57X81, Q5RBK0, Q5RDX4, Q62120, Q66H30, Q6R2W3, Q7KLI1, Q7LHG5, Q8CDM1, Q8K259, Q8N157, Q90179, Q91829, Q99315

Diamond homologs: A0A0P0VUY4, G3V8T1, O60016, O95931, P05205, P23198, P29227, P30658, P45968, P45973, P60889, P83916, P83917, Q10103, Q13185, Q14781, Q3TYA6, Q5F3W5, Q5KQL9, Q5R6X7, Q61686, Q6AYK9, Q8N8U2, Q8VDS3, Q94F87, Q99549, Q9AXT8, Q9D5D8, Q9WTK2, Q9Y232, Q9Y6F7, Q9Y6F8, G5EDE2, G5EET5, O43463, O54864, O95503, Q2NL30, Q339W7, Q5RB81

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

28 predictions. Top by Δscore:

Variant	Effect	Δscore
Y:17880088:A:AC	donor_gain	0.3300
Y:17880089:C:CC	donor_gain	0.3300
Y:17880088:ACTG:A	donor_gain	0.3200
Y:17880089:CTGC:C	donor_gain	0.3200
Y:17878470:C:G	acceptor_gain	0.3000
Y:17879370:C:CT	donor_gain	0.3000
Y:17878584:T:C	donor_gain	0.2700
Y:17879371:C:CT	donor_gain	0.2700
Y:17879350:C:A	donor_gain	0.2600
Y:17879249:A:C	donor_gain	0.2500
Y:17878576:T:TC	donor_gain	0.2400
Y:17879493:T:C	donor_gain	0.2400
Y:17879432:A:AC	donor_gain	0.2300
Y:17879433:C:CC	donor_gain	0.2300
Y:17879369:A:AC	donor_gain	0.2200
Y:17879922:TGTGC:T	donor_gain	0.2200
Y:17880089:CTG:C	donor_gain	0.2200
Y:17878824:T:TA	donor_gain	0.2100
Y:17878949:A:AC	donor_gain	0.2100
Y:17879015:T:TA	donor_gain	0.2100
Y:17879364:TGAAG:T	donor_gain	0.2100
Y:17879867:TCA:T	donor_gain	0.2100
Y:17878575:CT:C	donor_gain	0.2000
Y:17878577:TT:T	donor_gain	0.2000
Y:17878839:CAAA:C	donor_gain	0.2000
Y:17879428:ACTC:A	acceptor_gain	0.2000
Y:17879573:TTGG:T	donor_gain	0.2000
Y:17880208:T:TA	donor_gain	0.2000

AlphaMissense

3592 scored. Top likely-pathogenic:

dbSNP variants (sampled 20 via entrez): RS1271309712 (Y:17879787 C>T), RS1353961450 (Y:17879541 C>A), RS1418943806 (Y:17880714 GAC>G), RS1433258159 (Y:17879724 G>A), RS1603533537 (Y:17879961 T>C), RS1603533538 (Y:17880112 T>G), RS1603533539 (Y:17880119 C>A), RS1603533540 (Y:17880169 C>G), RS1603533541 (Y:17880214 C>T), RS1603533542 (Y:17880263 A>G), RS1603533543 (Y:17880542 G>T), RS1603533544 (Y:17880866 A>C), RS2520848168 (Y:17878165 G>C), RS2520848207 (Y:17880018 G>T), RS2520848260 (Y:17880501 C>CGTTTT)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (1): azoospermia (MONDO:0100459)

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
D053713	Azoospermia	C12.100.500.430.380; C12.100.750.700.380; C12.200.294.430.380

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

3 total (human), top 3 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	affects splicing, decreases expression	1
CGP 52608	affects binding, increases reaction	1
Aflatoxin B1	increases methylation	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT02307994	PHASE4	UNKNOWN	Clinical Research on Effectiveness and Safety of Treatment of Severe Oligospermia or Azoospermia With uFSH
NCT02275169	PHASE3	UNKNOWN	FSH Treatment for Non-obstructive Azoospermic Patients
NCT02544191	PHASE2	UNKNOWN	GnRHa Combined With hCG and hMG for Treatment of Patients With Non-obstructive Azoospermia
NCT03762967	PHASE2	UNKNOWN	Autologous Adipose-Derived Adult Stromal Vascular Cell Administration for Male Patients With Infertility
NCT02041910	PHASE1/PHASE2	UNKNOWN	Testicular Injection of Autologous Stem Cells for Treatment of Patients With Azoospermia
NCT00282477	Not specified	UNKNOWN	Trial to Evaluate Erectile Function, Fertility and Sperm Count in Male Cyclists Compared to Age Matched Controls
NCT00484081	Not specified	COMPLETED	Microdissection Testicular Sperm Extraction (MicroTESE) and IVF-ICSI Outcome in Non-Obstructive Azoospermia (NOA)
NCT00548977	Not specified	COMPLETED	Genetic Studies Spermatogenic Failure
NCT01375062	Not specified	COMPLETED	Obtaining Undifferentiated Cells From Testis Biopsy
NCT01509482	Not specified	COMPLETED	Insulin Resistance in Idiopathic Oligospermia and Azoospermia
NCT02008799	Not specified	UNKNOWN	Intra Testicular Artery Injection of Bone Marrow Stem Cell in Management of Azoospermia
NCT02339272	Not specified	COMPLETED	Study of Synapsis and Recombination in Male Meiosis and the Implications in Infertility
NCT02414295	Not specified	COMPLETED	Sperm Production in Kleinfelter Syndrome Patients After Mesenchymal Stem Cell Injection
NCT02418832	Not specified	RECRUITING	Testis Needle Aspiration of Sperm in Men With Azoospermia
NCT02617173	Not specified	UNKNOWN	The Effect of Low Electrical Current on Testicular Spermatocyte Count
NCT02773498	Not specified	TERMINATED	Comparison of Medical Results of Testicular Sperm Extraction by Conventional Surgery and Microsurgical Track
NCT03497728	Not specified	TERMINATED	Detection of Microdeletions in the Azoospermia Factor (AZF) Regions in Infertile Male Patients
NCT04675164	Not specified	COMPLETED	Laser Assisted Sperm Selection of Viable Immotile Testicular Sperm in Azoospermic Infertile Men
NCT05479474	Not specified	RECRUITING	Platelet Rich Plasma Testis Treatment for Infertile Men
NCT05628987	Not specified	RECRUITING	The Association of Gut Microbiota and Spermatogenic Dysfunction
NCT05866484	Not specified	COMPLETED	Testicular Sperm Aspiration (TESA) vs. Microfluidic Sperm Separation (MSS)
NCT06524258	Not specified	COMPLETED	Testicular Elastography for Microscopic Testicular Sperm Extraction
NCT06841328	Not specified	RECRUITING	Fertility Enhancement Through Regenerative Treatment in Ovaries and Testes
NCT06941922	Not specified	RECRUITING	Testicular Evaluation of Azoospermia Using Micro-Ultrasound
NCT07074015	Not specified	RECRUITING	IntelliWell: An AI-Assisted Imaging Platform for Detection and Location of Ultra-Rare Testicular Sperm in Surgical Specimens
NCT07357701	Not specified	RECRUITING	Identifying Genome Variants in Non-Obstructive Azoospermia (NOA) or Primary Ovarian Insufficiency (POI)
NCT07542626	Not specified	RECRUITING	Fertility Restoration With Autografting of Cryopreserved Immature Testicular Tissue