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.

• not_specified (35 variants)

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. These statistics are base on transcript: NM_001397900.1. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			35			35
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	35	0	0

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