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CDKL5 cyclin dependent kinase like 5 [ Homo sapiens (human) ]

Gene ID: 6792, updated on 5-Jul-2025
Official Symbol
CDKL5provided by HGNC
Official Full Name
cyclin dependent kinase like 5provided by HGNC
Primary source
HGNC:HGNC:11411
See related
Ensembl:ENSG00000008086 MIM:300203; AllianceGenome:HGNC:11411
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
DEE2; ISSX; STK9; EIEE2; CFAP247
Summary
This gene is a member of Ser/Thr protein kinase family and encodes a phosphorylated protein with protein kinase activity. Mutations in this gene have been associated with X-linked infantile spasm syndrome (ISSX), also known as X-linked West syndrome, and Rett syndrome (RTT). Alternate transcriptional splice variants have been characterized. [provided by RefSeq, Jul 2008]
Expression
Broad expression in brain (RPKM 11.1), lung (RPKM 3.0) and 18 other tissues See more
Orthologs
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See CDKL5 in Genome Data Viewer
Location:
Xp22.13
Exon count:
23
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (18425608..18653629)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (18008223..18236232)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (18443728..18671749)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene Scm polycomb group protein like 2 Neighboring gene uncharacterized LOC124905253 Neighboring gene thymosin beta 10 pseudogene 2 Neighboring gene Sharpr-MPRA regulatory region 2020 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20685 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:18460197-18460698 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:18460699-18461198 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:18487190-18487391 Neighboring gene uncharacterized LOC124905289 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chrX:18583809-18584371 Neighboring gene gap junction protein alpha 6, pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chrX:18658784-18658953 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:18667451-18668199 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:18679457-18680008 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:18693026-18693212 Neighboring gene tRNA-Val (anticodon TAC) 1-2 Neighboring gene retinoschisin 1 Neighboring gene PPEF1 antisense RNA 1 Neighboring gene protein phosphatase with EF-hand domain 1

Go to nucleotide: Graphics FASTA GenBank

  • Project title: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

Related articles in PubMed

  1. Epileptic encephalopathy and atypical Rett syndrome with mutations in CDKL5: clinical and molecular characterization of two Brazilian patients. Ermel EL, et al. Arq Neuropsiquiatr, 2013 Jun. PMID 23828526
  2. iPS cells to model CDKL5-related disorders. Amenduni M, et al. Eur J Hum Genet, 2011 Dec. PMID 21750574, Free PMC Article
  3. Clinical phenotype of 5 females with a CDKL5 mutation. Stalpers XL, et al. J Child Neurol, 2012 Jan. PMID 21765152
  4. CDKL5 alterations lead to early epileptic encephalopathy in both genders. Liang JS, et al. Epilepsia, 2011 Oct. PMID 21770923
  5. Mutation screening of the CDKL5 gene in cryptogenic infantile intractable epilepsy and review of clinical sensitivity. Intusoma U, et al. Eur J Paediatr Neurol, 2011 Sep. PMID 21775177

See all (141) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Novel CDKL5 targets identified in human iPSC-derived neurons.
    Title: Novel CDKL5 targets identified in human iPSC-derived neurons.
  2. First report of Tunisian patients with CDKL5-related encephalopathy.
    Title: First report of Tunisian patients with CDKL5-related encephalopathy.
  3. Growth patterns in individuals with CDKL5 deficiency disorder.
    Title: Growth patterns in individuals with CDKL5 deficiency disorder.
  4. CDKL5 deficiency disorder and other infantile-onset genetic epilepsies.
    Title: CDKL5 deficiency disorder and other infantile-onset genetic epilepsies.
  5. CDKL5 Deficiency Disorder: Some Lessons Learned 20 Years After the First Description.
    Title: CDKL5 Deficiency Disorder: Some Lessons Learned 20 Years After the First Description.
  6. Epilepsy-linked kinase CDKL5 phosphorylates voltage-gated calcium channel Cav2.3, altering inactivation kinetics and neuronal excitability.
    Title: Epilepsy-linked kinase CDKL5 phosphorylates voltage-gated calcium channel Cav2.3, altering inactivation kinetics and neuronal excitability.
  7. CDKL5-mediated developmental tuning of neuronal excitability and concomitant regulation of transcriptome.
    Title: CDKL5-mediated developmental tuning of neuronal excitability and concomitant regulation of transcriptome.
  8. The development, content and response process validation of a caregiver-reported severity measure for CDKL5 deficiency disorder.
    Title: The development, content and response process validation of a caregiver-reported severity measure for CDKL5 deficiency disorder.
  9. CDKL5 deficiency disorder: progressive brain atrophy may be part of the syndrome.
    Title: CDKL5 deficiency disorder: progressive brain atrophy may be part of the syndrome.
  10. CDKL5 Deficiency Disorder Without Epilepsy.
    Title: CDKL5 Deficiency Disorder Without Epilepsy.
Submit: New GeneRIF Correction See all GeneRIFs (110)

Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Angelman syndrome-like
MedGen: CN128785 GeneReviews: Not available
Compare labs
Developmental and epileptic encephalopathy, 2
MedGen: C4750718 OMIM: 300672 GeneReviews: CDKL5 Deficiency Disorder
Compare labs

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated 2012-07-12)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated 2012-07-12)

ClinGen Genome Curation PagePubMed

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables ATP binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables ATP binding IEA
Inferred from Electronic Annotation
more info
  
enables cyclin-dependent protein serine/threonine kinase activity IEA
Inferred from Electronic Annotation
more info
  
enables kinase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables kinase activity IEA
Inferred from Electronic Annotation
more info
  
enables nucleotide binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein kinase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein kinase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein kinase activity IEA
Inferred from Electronic Annotation
more info
  
enables protein serine kinase activity IEA
Inferred from Electronic Annotation
more info
  
enables protein serine/threonine kinase activity IEA
Inferred from Electronic Annotation
more info
  
enables protein serine/threonine kinase activity TAS
Traceable Author Statement
more info
 PubMed 
enables small GTPase binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables transferase activity IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in modulation of chemical synaptic transmission IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in modulation of chemical synaptic transmission IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in neuron migration ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of Rac protein signal transduction ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of axon extension IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of axon extension ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of dendrite morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in regulation of cell cycle IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of cilium assembly IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of dendrite development IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of dendrite development ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in regulation of postsynapse organization IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of postsynapse organization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in cell projection IEA
Inferred from Electronic Annotation
more info
  
located_in centrosome IDA
Inferred from Direct Assay
more info
 PubMed 
located_in centrosome IEA
Inferred from Electronic Annotation
more info
  
located_in ciliary basal body IDA
Inferred from Direct Assay
more info
 PubMed 
located_in ciliary tip IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
  
located_in cytoskeleton IEA
Inferred from Electronic Annotation
more info
  
is_active_in dendrite cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in dendrite cytoplasm ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in dendritic growth cone ISS
Inferred from Sequence or Structural Similarity
more info
  
is_active_in glutamatergic synapse IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in glutamatergic synapse IMP
Inferred from Mutant Phenotype
more info
 PubMed 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  
colocalizes_with ruffle membrane ISS
Inferred from Sequence or Structural Similarity
more info
  
Preferred Names
cyclin-dependent kinase-like 5
Names
cyclin dependent kinase 5 transcript
serine/threonine kinase 9
serine/threonine-protein kinase 9
NP_001032420.1
NP_001310218.1
NP_003150.1

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_008475.1 RefSeqGene

    Range
    5004..219592
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001037343.2 → NP_001032420.1  cyclin-dependent kinase-like 5 isoform 1

    See identical proteins and their annotated locations for NP_001032420.1

    Status: REVIEWED

    Source sequence(s)
    AI286150, AL704691, AY217744, BC036091
    Consensus CDS
    CCDS14186.1
    UniProtKB/TrEMBL
    A0A669KBC2
    Related
    ENSP00000369325.3, ENST00000379989.6
    Conserved Domains (2) summary
    smart00220
    Location:13 → 297
    S_TKc; Serine/Threonine protein kinases, catalytic domain
    cd07848
    Location:11 → 297
    STKc_CDKL5; Catalytic domain of the Serine/Threonine Kinase, Cyclin-Dependent protein Kinase Like 5

  2. NM_001323289.2 → NP_001310218.1  cyclin-dependent kinase-like 5 isoform 2

    Status: REVIEWED

    Source sequence(s)
    AL109798, AW452901, HQ171445, Z92542
    Consensus CDS
    CCDS83458.1
    UniProtKB/Swiss-Prot
    G9B9X4, O76039, Q14198, Q5H985, Q8IYC7, Q9UJL6
    UniProtKB/TrEMBL
    A0A669KBC2
    Related
    ENSP00000485244.1, ENST00000623535.2
    Conserved Domains (1) summary
    cd07848
    Location:11 → 297
    STKc_CDKL5; Catalytic domain of the Serine/Threonine Kinase, Cyclin-Dependent protein Kinase Like 5

  3. NM_003159.3 → NP_003150.1  cyclin-dependent kinase-like 5 isoform 1

    See identical proteins and their annotated locations for NP_003150.1

    Status: REVIEWED

    Source sequence(s)
    AI286150, AY217744, BC010966
    Consensus CDS
    CCDS14186.1
    UniProtKB/TrEMBL
    A0A669KBC2
    Related
    ENSP00000369332.3, ENST00000379996.7
    Conserved Domains (2) summary
    smart00220
    Location:13 → 297
    S_TKc; Serine/Threonine protein kinases, catalytic domain
    cd07848
    Location:11 → 297
    STKc_CDKL5; Catalytic domain of the Serine/Threonine Kinase, Cyclin-Dependent protein Kinase Like 5

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    18425608..18653629
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    18008223..18236232
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O76039.2 GenPept UniProtKB/Swiss-Prot:O76039

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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