CDKL1

cyclin dependent kinase like 1, the group of Cyclin dependent kinases

Basic information

Region (hg38): 14:50326265-50416461

Links

ENSG00000100490 ∙ NCBI:8814 ∙ OMIM:603441 ∙ HGNC:1781 ∙ Uniprot:Q00532 ∙ 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 CDKL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDKL1 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			21			21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	0	0

Variants in CDKL1

This is a list of pathogenic ClinVar variants found in the CDKL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-50341089-G-A		not specified	Uncertain significance (Mar 25, 2024)
14-50341124-A-G		not specified	Uncertain significance (Jan 08, 2025)
14-50341149-C-T		not specified	Uncertain significance (Sep 01, 2021)
14-50341157-G-A		not specified	Uncertain significance (Feb 06, 2025)
14-50342182-G-A		not specified	Uncertain significance (Mar 28, 2023)
14-50345027-A-T		not specified	Uncertain significance (Dec 15, 2023)
14-50345042-C-T		not specified	Uncertain significance (Dec 14, 2024)
14-50345048-G-A		not specified	Uncertain significance (Jan 10, 2022)
14-50345053-G-A		not specified	Uncertain significance (Feb 01, 2025)
14-50359029-C-T		not specified	Uncertain significance (Feb 26, 2025)
14-50359092-G-C		not specified	Uncertain significance (Oct 31, 2024)
14-50359098-G-A		not specified	Uncertain significance (Dec 03, 2021)
14-50359100-T-A		not specified	Uncertain significance (Mar 13, 2023)
14-50359137-G-T		not specified	Uncertain significance (Nov 14, 2024)
14-50359139-T-A		not specified	Uncertain significance (Jul 30, 2023)
14-50359142-T-C		not specified	Uncertain significance (May 20, 2024)
14-50395706-G-A		not specified	Uncertain significance (May 20, 2024)
14-50395712-G-C		not specified	Uncertain significance (Oct 12, 2022)
14-50395717-T-G		not specified	Uncertain significance (Sep 26, 2023)
14-50395746-G-T		not specified	Uncertain significance (Oct 03, 2023)
14-50395759-T-A		not specified	Uncertain significance (Mar 20, 2024)
14-50395759-T-G		not specified	Uncertain significance (Oct 19, 2024)
14-50395790-C-T		not specified	Uncertain significance (Mar 20, 2024)
14-50395843-T-G		not specified	Uncertain significance (Aug 16, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CDKL1	protein_coding	protein_coding	ENST00000395834	9	86870

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.50e-7	0.738	125502	0	246	125748	0.000979

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.818	165	197	0.836	0.0000105	2354
Missense in Polyphen		47	62.209	0.75552		701
Synonymous	0.383	72	76.3	0.944	0.00000428	672
Loss of Function	1.28	13	19.0	0.683	9.74e-7	224

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000271	0.000271
Ashkenazi Jewish	0.000397	0.000397
East Asian	0.000327	0.000326
Finnish	0.00402	0.00403
European (Non-Finnish)	0.000671	0.000668
Middle Eastern	0.000327	0.000326
South Asian	0.00184	0.00183
Other	0.00180	0.00179

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.791
• rvis_EVS: 0.6
• rvis_percentile_EVS: 82.66

Haploinsufficiency Scores

• pHI: 0.190
• hipred: N
• hipred_score: 0.344
• ghis: 0.429

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0167

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cdkl1

Zebrafish Information Network

• Gene name: cdkl1
• Affected structure: post-vent region
• Phenotype tag: abnormal
• Phenotype quality: kinked

Gene ontology

• Biological process: protein phosphorylation;heart development;regulation of cell cycle;regulation of cilium assembly
• Cellular component: nucleus;nucleoplasm;cytoplasm;ciliary transition zone;intracellular membrane-bounded organelle;extracellular exosome
• Molecular function: cyclin-dependent protein serine/threonine kinase activity;ATP binding