CDKL3

cyclin dependent kinase like 3, the group of Cyclin dependent kinases

Basic information

Region (hg38): 5:134286350-134371047

Links

ENSG00000006837 ∙ NCBI:51265 ∙ OMIM:608459 ∙ HGNC:15483 ∙ Uniprot:Q8IVW4 ∙ 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 CDKL3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDKL3 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			42			42
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	42	0	2

Variants in CDKL3

This is a list of pathogenic ClinVar variants found in the CDKL3 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-134302616-C-T		not specified	Uncertain significance (Mar 04, 2025)
5-134302622-G-C		not specified	Uncertain significance (Mar 21, 2023)
5-134302623-T-A		not specified	Uncertain significance (Nov 30, 2022)
5-134304450-C-T		not specified	Uncertain significance (May 29, 2024)
5-134304525-T-C		not specified	Uncertain significance (Mar 25, 2024)
5-134304540-C-T		not specified	Uncertain significance (Apr 04, 2024)
5-134306639-A-G			Benign (May 30, 2018)
5-134306652-T-C		not specified	Uncertain significance (Oct 02, 2023)
5-134306677-G-A		not specified	Uncertain significance (Jan 22, 2025)
5-134306678-T-A		not specified	Uncertain significance (Dec 04, 2023)
5-134308191-G-C		not specified	Uncertain significance (Dec 06, 2024)
5-134308226-C-T		not specified	Uncertain significance (May 28, 2024)
5-134308273-T-C		not specified	Uncertain significance (Jan 22, 2025)
5-134308319-A-T		not specified	Uncertain significance (Jun 07, 2024)
5-134308322-T-C		not specified	Uncertain significance (Oct 14, 2023)
5-134308333-T-C		not specified	Uncertain significance (Oct 05, 2021)
5-134308377-C-A		not specified	Uncertain significance (Jun 12, 2023)
5-134308400-C-G		not specified	Uncertain significance (May 03, 2023)
5-134308442-T-C		not specified	Uncertain significance (Oct 05, 2021)
5-134308444-G-A		not specified	Uncertain significance (Feb 11, 2025)
5-134308462-A-G		not specified	Uncertain significance (Feb 06, 2023)
5-134308579-C-T		not specified	Uncertain significance (Jan 13, 2023)
5-134308581-A-C		not specified	Uncertain significance (Feb 08, 2025)
5-134308660-C-G		not specified	Uncertain significance (May 20, 2024)
5-134308718-T-C			Benign (Jun 08, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CDKL3	protein_coding	protein_coding	ENST00000265334	12	165434

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.26e-12	0.232	124530	1	117	124648	0.000473

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.388	245	263	0.933	0.0000122	3886
Missense in Polyphen		79	95.294	0.82901		1495
Synonymous	1.07	75	87.8	0.854	0.00000427	1043
Loss of Function	0.966	21	26.4	0.797	0.00000140	395

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000561	0.000519
Ashkenazi Jewish	0.00	0.00
East Asian	0.00314	0.00279
Finnish	0.00	0.00
European (Non-Finnish)	0.000441	0.000407
Middle Eastern	0.00314	0.00279
South Asian	0.000335	0.000261
Other	0.000357	0.000330

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.104

Intolerance Scores

• loftool: 0.647
• rvis_EVS: 0.33
• rvis_percentile_EVS: 73.41

Haploinsufficiency Scores

• pHI: 0.186
• hipred: N
• hipred_score: 0.213
• ghis: 0.447

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.357

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cdkl3

Gene ontology

• Biological process: cellular protein modification process;protein phosphorylation;negative regulation of axon extension;positive regulation of dendrite morphogenesis;regulation of cell cycle;dendrite extension
• Cellular component: nucleus;cytoplasm
• Molecular function: protein kinase activity;cyclin-dependent protein serine/threonine kinase activity;protein binding;ATP binding