CDYL2

chromodomain Y like 2

Basic information

Region (hg38): 16:80597907-80804598

Links

ENSG00000166446 ∙ NCBI:124359 ∙ OMIM:618816 ∙ HGNC:23030 ∙ Uniprot:Q8N8U2 ∙ 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 CDYL2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDYL2 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					2	2
missense			26	1		27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	1	2

Variants in CDYL2

This is a list of pathogenic ClinVar variants found in the CDYL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-80604518-C-T		not specified	Uncertain significance (Aug 01, 2022)
16-80604537-C-T		not specified	Uncertain significance (Nov 29, 2023)
16-80608211-G-A		not specified	Uncertain significance (Nov 22, 2022)
16-80612634-C-A		not specified	Uncertain significance (Jul 20, 2021)
16-80612684-C-T		not specified	Uncertain significance (Jun 03, 2024)
16-80612779-C-A			Benign (Dec 31, 2019)
16-80612793-C-G		not specified	Uncertain significance (Dec 17, 2023)
16-80620782-G-A		not specified	Uncertain significance (Feb 10, 2022)
16-80620818-C-T		not specified	Uncertain significance (Oct 30, 2023)
16-80620839-G-C		not specified	Uncertain significance (Sep 01, 2021)
16-80620913-G-A		not specified	Uncertain significance (Jan 04, 2024)
16-80620920-G-A		not specified	Uncertain significance (Apr 07, 2023)
16-80633047-G-A		not specified	Uncertain significance (Jan 27, 2022)
16-80633049-C-A		not specified	Uncertain significance (Feb 12, 2024)
16-80633070-C-T			Benign (Dec 31, 2019)
16-80633152-T-C		not specified	Uncertain significance (Jul 11, 2023)
16-80633173-T-C		not specified	Uncertain significance (Jun 28, 2022)
16-80633194-A-G		not specified	Uncertain significance (Aug 08, 2023)
16-80633233-G-T		not specified	Uncertain significance (May 26, 2023)
16-80684556-G-C		not specified	Uncertain significance (Feb 12, 2024)
16-80684605-A-T		not specified	Uncertain significance (Apr 19, 2023)
16-80684666-G-A		not specified	Uncertain significance (May 15, 2023)
16-80684755-C-G		not specified	Uncertain significance (Dec 15, 2023)
16-80684795-T-C		not specified	Uncertain significance (Jun 30, 2022)
16-80684801-T-C		not specified	Uncertain significance (Dec 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CDYL2	protein_coding	protein_coding	ENST00000570137	7	206424

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0193	0.980	125739	0	9	125748	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.107	305	300	1.02	0.0000187	3301
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000616	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000530	0.0000527
Middle Eastern	0.00	0.00
South Asian	0.0000367	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.107

Intolerance Scores

• loftool: 0.176
• rvis_EVS: -1.17
• rvis_percentile_EVS: 5.99

Haploinsufficiency Scores

• pHI: 0.569
• hipred: Y
• hipred_score: 0.653
• ghis: 0.571

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.237

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cdyl2

Gene ontology

• Biological process: negative regulation of nucleic acid-templated transcription
• Cellular component: nucleus
• Molecular function: transcription corepressor activity;catalytic activity;protein binding;methylated histone binding