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

    Gene ID: 6792, updated on 27-Nov-2024

    Summary

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    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
    mouse all
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    Genomic context

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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

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    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 (142) 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 (111)

    Phenotypes

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    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
    		not available
    Developmental and epileptic encephalopathy, 2
    MedGen: C4750718 OMIM: 300672 GeneReviews: CDKL5 Deficiency Disorder
    		not available

    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

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ATP binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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 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 serine 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
    		  
    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 positive regulation of dendritic spine development IEA
    Inferred from Electronic Annotation
    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 centrosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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 
    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 perinuclear region of cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in postsynaptic density, intracellular component IEA
    Inferred from Electronic Annotation
    more info
    		  
    colocalizes_with ruffle membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    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

    NCBI Reference Sequences (RefSeq)

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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.

    Chemical Information
    Medical
    Molecular Biology Databases
    Research Materials
    Tools