CDKL4

cyclin dependent kinase like 4, the group of Cyclin dependent kinases

Basic information

Region (hg38): 2:39168045-39243983

Links

ENSG00000205111 ∙ NCBI:344387 ∙ ∙ HGNC:19287 ∙ Uniprot:Q5MAI5 ∙ 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 CDKL4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDKL4 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			19			19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	0	0

Variants in CDKL4

This is a list of pathogenic ClinVar variants found in the CDKL4 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-39179219-G-A		not specified	Uncertain significance (Jun 30, 2024)
2-39179257-A-G		not specified	Uncertain significance (Mar 06, 2025)
2-39184623-C-G		not specified	Uncertain significance (Mar 23, 2023)
2-39184631-T-C		not specified	Uncertain significance (Dec 03, 2021)
2-39187629-T-C		not specified	Uncertain significance (Dec 15, 2023)
2-39190410-C-T		not specified	Uncertain significance (Jan 23, 2024)
2-39190413-C-T		not specified	Uncertain significance (May 14, 2024)
2-39190418-G-A		not specified	Uncertain significance (Feb 27, 2025)
2-39190433-T-C		not specified	Uncertain significance (Jan 26, 2025)
2-39190445-A-G		not specified	Uncertain significance (Jan 26, 2025)
2-39190452-G-A		not specified	Uncertain significance (Aug 14, 2024)
2-39190455-C-G		not specified	Uncertain significance (Nov 07, 2024)
2-39190457-C-T		not specified	Uncertain significance (Dec 28, 2022)
2-39190482-C-T		not specified	Uncertain significance (Mar 07, 2023)
2-39204613-A-C		not specified	Uncertain significance (Feb 27, 2024)
2-39213404-T-C		not specified	Uncertain significance (Sep 20, 2023)
2-39213448-G-T		not specified	Uncertain significance (Jun 21, 2023)
2-39225854-T-C		not specified	Uncertain significance (Sep 10, 2024)
2-39225935-T-G		not specified	Uncertain significance (Oct 12, 2024)
2-39229418-C-T		not specified	Uncertain significance (Dec 19, 2022)
2-39229430-A-T		not specified	Uncertain significance (Dec 19, 2022)
2-39229487-C-T		not specified	Uncertain significance (Jul 25, 2023)
2-39229505-T-C		not specified	Uncertain significance (Mar 25, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CDKL4	protein_coding	protein_coding	ENST00000378803	8	53943

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.01e-14	0.00736	125383	2	362	125747	0.00145

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0158	162	163	0.997	0.00000802	2073
Missense in Polyphen		63	60.978	1.0332		802
Synonymous	0.251	54	56.4	0.957	0.00000297	574
Loss of Function	-0.551	19	16.6	1.15	8.83e-7	209

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00387	0.00387
Ashkenazi Jewish	0.00	0.00
East Asian	0.0101	0.0101
Finnish	0.00	0.00
European (Non-Finnish)	0.000213	0.000176
Middle Eastern	0.0101	0.0101
South Asian	0.000908	0.000850
Other	0.000660	0.000652

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0869

Intolerance Scores

• loftool: 0.711
• rvis_EVS: 0.04
• rvis_percentile_EVS: 57.15

Haploinsufficiency Scores

• pHI: 0.0934
• hipred: N
• hipred_score: 0.144
• ghis: 0.387

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0449

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cdkl4

Gene ontology

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