CDKL2

cyclin dependent kinase like 2, the group of Cyclin dependent kinases

Basic information

Region (hg38): 4:75576495-75630716

Links

ENSG00000138769 ∙ NCBI:8999 ∙ OMIM:603442 ∙ HGNC:1782 ∙ Uniprot:Q92772 ∙ 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 CDKL2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDKL2 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			26			26
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	0	0

Variants in CDKL2

This is a list of pathogenic ClinVar variants found in the CDKL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-75581837-T-C		not specified	Uncertain significance (May 25, 2022)
4-75596954-T-G		not specified	Likely benign (May 01, 2024)
4-75596965-C-A		not specified	Uncertain significance (Jun 09, 2022)
4-75597053-C-T		not specified	Uncertain significance (May 23, 2023)
4-75597184-C-G		not specified	Uncertain significance (Nov 18, 2023)
4-75597205-T-A		not specified	Uncertain significance (Mar 04, 2024)
4-75597232-G-T		not specified	Uncertain significance (Mar 07, 2023)
4-75598105-A-G		not specified	Uncertain significance (Feb 28, 2023)
4-75598117-T-A		not specified	Uncertain significance (Mar 04, 2024)
4-75598186-A-G		not specified	Uncertain significance (Sep 06, 2022)
4-75600361-T-A		not specified	Uncertain significance (Apr 17, 2024)
4-75603840-C-T		not specified	Uncertain significance (Sep 06, 2022)
4-75603858-G-A		not specified	Uncertain significance (Apr 19, 2024)
4-75603933-C-T		not specified	Uncertain significance (Jun 05, 2023)
4-75603935-T-G		not specified	Uncertain significance (Jan 25, 2023)
4-75603953-T-C		not specified	Uncertain significance (Jan 17, 2023)
4-75605594-T-A		not specified	Uncertain significance (Jan 29, 2024)
4-75607211-G-T		not specified	Uncertain significance (Jul 15, 2021)
4-75607268-C-T		not specified	Uncertain significance (Apr 25, 2022)
4-75607279-C-T		not specified	Uncertain significance (Jul 14, 2023)
4-75607354-T-C		not specified	Uncertain significance (Mar 31, 2024)
4-75607355-G-C		not specified	Uncertain significance (Aug 08, 2022)
4-75614311-C-T		not specified	Uncertain significance (Nov 18, 2022)
4-75614325-A-C		not specified	Uncertain significance (Sep 14, 2022)
4-75614361-G-C		not specified	Uncertain significance (Sep 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CDKL2	protein_coding	protein_coding	ENST00000429927	10	52686

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.10e-17	0.00484	123331	18	2398	125747	0.00965

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.246	263	252	1.04	0.0000118	3271
Missense in Polyphen		70	73.715	0.9496		966
Synonymous	-0.0988	91	89.8	1.01	0.00000457	894
Loss of Function	-0.113	25	24.4	1.02	0.00000138	319

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00793	0.00783
Ashkenazi Jewish	0.00429	0.00398
East Asian	0.00442	0.00414
Finnish	0.0219	0.0219
European (Non-Finnish)	0.0137	0.0134
Middle Eastern	0.00442	0.00414
South Asian	0.00164	0.00141
Other	0.0128	0.0121

dbNSFP

Source: dbNSFP

• Pathway: EMT transition in Colorectal Cancer (Consensus)

Recessive Scores

• pRec: 0.178

Intolerance Scores

• loftool: 0.714
• rvis_EVS: -0.07
• rvis_percentile_EVS: 48.54

Haploinsufficiency Scores

• pHI: 0.0994
• hipred: Y
• hipred_score: 0.515
• ghis: 0.527

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0385

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cdkl2
• Phenotype: immune system phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: protein phosphorylation;signal transduction;sex differentiation;regulation of cell cycle
• Cellular component: nucleus;cytoplasm;centrosome
• Molecular function: protein kinase activity;cyclin-dependent protein serine/threonine kinase activity;ATP binding