CDYL2

protein-coding

chromodomain Y like 2

Gene summary

Predicted to enable transcription corepressor activity. Predicted to be involved in chromatin organization and negative regulation of DNA-templated transcription. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_152342.4

Inheritance

—

ClinVar variants

U:76B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.32

Max pathogenic AF

—

Genomic locus

chr16:80,597,907-80,804,598

External References & Databases

Ensembl (ENSG00000166446)

Transcript & Mutation Effects

hg38 • Region Span ~206.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CDYL2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 71

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_152342.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar		2 clinvar	4
missense			73 clinvar	1 clinvar		74
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	76	1	2	79

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 14 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_152342.4	RefSeq	NP_689555.2	7	MANE Select
ENST00000570137.7	Ensembl	ENSP00000476295.1	7	MANE Select
ENST00000562812.5	Ensembl	ENSP00000454546.1	8	Standard
ENST00000562812.6	Ensembl	ENSP00000454546.1	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

negative regulation of nucleic acid-templated transcription

Molecular Function

transcription corepressor activity
catalytic activity
protein binding
methylated histone binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000570137
Coding exons: 7
Length: 206424
Individuals with no LoFs: 125739
Homozygous LoFs: 0
Heterozygous LoFs: 9
Defined: 125748
p: 0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.107	305	300	1.02	0.0000187	3301
Missense (PolyPhen)		112	146.19	0.76611		1626
Synonymous	-2.80	172	131	1.31	0.00000903	979
Loss of Function	2.95	7	21.9	0.319	0.00000139	245

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.000053	0.000053	rare
South Asian	0.000037	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.107

Intolerance Scores

LoFtool: 0.176
RVIS EVS: -1.17
RVIS percentile EVS: 5.99

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: N
Indispensability score: 0.237

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium