CDYL

chromodomain Y like

Basic information

Region (hg38): 6:4706159-4955551

Links

ENSG00000153046 ∙ NCBI:9425 ∙ OMIM:603778 ∙ HGNC:1811 ∙ Uniprot:Q9Y232 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CDYL gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDYL gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			25			25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2		1	3
Total	0	0	27	0	1

Variants in CDYL

This is a list of pathogenic ClinVar variants found in the CDYL region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
6-4891860-C-T		not specified	Uncertain significance (Jan 09, 2024)
6-4891876-A-C		not specified	Uncertain significance (Dec 20, 2023)
6-4891932-C-G		not specified	Uncertain significance (Jul 07, 2024)
6-4891948-C-T		not specified	Uncertain significance (Nov 08, 2022)
6-4891995-A-C		not specified	Uncertain significance (Jun 16, 2024)
6-4892046-A-G		not specified	Uncertain significance (Sep 20, 2023)
6-4892067-C-T		not specified	Uncertain significance (Sep 09, 2024)
6-4892076-C-T		not specified	Uncertain significance (Mar 27, 2023)
6-4892077-G-A		not specified	Uncertain significance (Jun 07, 2024)
6-4892100-T-A		not specified	Uncertain significance (Jul 09, 2021)
6-4892133-G-T		not specified	Uncertain significance (Oct 26, 2022)
6-4892148-G-A		not specified	Uncertain significance (Jul 16, 2024)
6-4892157-G-A		not specified	Uncertain significance (May 11, 2022)
6-4892167-G-T		not specified	Uncertain significance (Sep 30, 2024)
6-4892196-G-A		not specified	Uncertain significance (Mar 13, 2023)
6-4892226-G-C		not specified	Uncertain significance (Mar 19, 2024)
6-4892232-G-T		not specified	Uncertain significance (Mar 19, 2024)
6-4892250-G-A		not specified	Uncertain significance (Jul 09, 2021)
6-4892319-C-T		not specified	Uncertain significance (Jan 06, 2023)
6-4892340-A-G		not specified	Uncertain significance (Oct 01, 2024)
6-4892349-A-G		not specified	Uncertain significance (Feb 07, 2023)
6-4935529-A-C		not specified	Uncertain significance (Mar 25, 2024)
6-4935547-A-G		not specified	Uncertain significance (Sep 21, 2023)
6-4935548-A-G		not specified	Uncertain significance (Nov 03, 2022)
6-4935564-A-G		not specified	Uncertain significance (Oct 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CDYL	protein_coding	protein_coding	ENST00000397588	7	249393

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.995	0.00496	125726	0	2	125728	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.35	205	324	0.632	0.0000195	3611
Missense in Polyphen		21	89.536	0.23454		1102
Synonymous	-0.577	139	131	1.06	0.00000913	1039
Loss of Function	3.95	1	20.1	0.0497	0.00000104	253

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.000103	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000881	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Isoform 2: Chromatin reader protein that recognizes and binds histone H3 trimethylated at 'Lys-9', dimethylated at 'Lys- 27' and trimethylated at 'Lys-27' (H3K9me3, H3K27me2 and H3K27me3, respectively) (PubMed:19808672, PubMed:28402439). Part of multimeric repressive chromatin complexes, where it is required for transmission and restoration of repressive histone marks, thereby preserving the epigenetic landscape (PubMed:28402439). Required for chromatin targeting and maximal enzymatic activity of Polycomb repressive complex 2 (PRC2); acts as a positive regulator of PRC2 activity by bridging the pre-existing histone H3K27me3 and newly recruited PRC2 on neighboring nucleosomes (PubMed:22009739). Acts as a corepressor for REST by facilitating histone-lysine N- methyltransferase EHMT2 recruitment and H3K9 dimethylation at REST target genes for repression (PubMed:19061646). Involved X chromosome inactivation in females: recruited to Xist RNA-coated X chromosome and facilitates propagation of H3K9me2 by anchoring EHMT2 (By similarity). Required for neuronal migration during brain development by repressing expression of RHOA (By similarity). In addition to act as a chromatin reader, acts as a hydro-lyase (PubMed:28803779). Shows crotonyl-coA hydratase activity by mediating the conversion of crotonyl-CoA ((2E)- butenoyl-CoA) to beta-hydroxybutyryl-CoA (3-hydroxybutanoyl-CoA), thereby acting as a negative regulator of histone crotonylation (PubMed:28803779). Histone crotonylation is required during spermatogenesis; down-regulation of histone crotonylation by CDYL regulates the reactivation of sex chromosome-linked genes in round spermatids and histone replacement in elongating spermatids (By similarity). {ECO:0000250|UniProtKB:Q9WTK2, ECO:0000269|PubMed:19061646, ECO:0000269|PubMed:19808672, ECO:0000269|PubMed:22009739, ECO:0000269|PubMed:28402439, ECO:0000269|PubMed:28803779}.; FUNCTION: Isoform 3: Not able to recognize and bind histone H3K9me3, histone H3K27me2 and histone H3K27me3, due to the absence of the chromo domain (PubMed:19808672). Acts as a negative regulator of isoform 2 by displacing isoform 2 from chromatin. {ECO:0000269|PubMed:19808672}.

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.634
• rvis_EVS: -1.57
• rvis_percentile_EVS: 3.14

Haploinsufficiency Scores

• pHI: 0.520
• hipred: Y
• hipred_score: 0.575
• ghis: 0.670

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.950

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cdyl
• Phenotype: cellular phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: spermatogenesis;spermatid development;random inactivation of X chromosome;negative regulation of peptidyl-lysine crotonylation;negative regulation of nucleic acid-templated transcription
• Cellular component: nucleus;chromosome;nuclear speck
• Molecular function: chromatin binding;transcription corepressor activity;protein binding;protein binding, bridging;methylated histone binding;crotonyl-CoA hydratase activity