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Relevance to Autism

A complex de novo chromosomal rearrangement disrupting the CELF4 gene was identified in a male patient with borderline IQ, developmental and behavioral disorders (inlcuding autistic behavior), myopia, obesity, and febrile seizures in childhood (Halgren et al., 2012). Two de novo loss-of-function (LoF) variants in this gene have been identified in ASD probands (Krumm et al., 2015; Lim et al., 2017). A familial 18q12.2 deletion with a distal breakpoint within intron 2 of the CELF4 gene was identified in a 7-year-old female proband diagnosed with autism and syndromic intellectual disability and her mother, who presented with intellectual disability and autistic behavior (Barone et al., 2017).

Molecular Function

RNA-binding protein implicated in the regulation of pre-mRNA alternative splicing. Mediates exon inclusion and/or exclusion in pre-mRNA that are subject to tissue-specific and developmentally regulated alternative splicing. When expressed ubiquitously, CELF4 is strongly expressed in the cerebellum, hippocampus, amygdala, temporal and frontal cortex and frontal lobes.

External Links

        

References

Type
Title
Type of Disorder
Associated Disorders
Author, Year
Primary
Haploinsufficiency of CELF4 at 18q12.2 is associated with developmental and behavioral disorders, seizures, eye manifestations, and obesity.
ID
DD
Support
Aberrant sodium channel activity in the complex seizure disorder of Celf4 mutant mice.
Support
Inherited and De Novo Genetic Risk for Autism Impacts Shared Networks.
ASD
Support
Etiology of a genetically complex seizure disorder in Celf4 mutant mice.
Support
Risks and Recommendations in Prenatally Detected De Novo Balanced Chromosomal Rearrangements from Assessment of Long-Term Outcomes.
Epilepsy/seizures, ODD, behavioral abnormalities,
Support
Support
Complex seizure disorder caused by Brunol4 deficiency in mice.
Support
Rates, distribution and implications of postzygotic mosaic mutations in autism spectrum disorder.
ASD
Support
Integrating de novo and inherited variants in 42
ASD
Support
Familial 18q12.2 deletion supports the role of RNA-binding protein CELF4 in autism spectrum disorders.
ASD/autistic features, ID
Epilepsy/seizures
Support
Prevalence and phenotypic impact of rare potentially damaging variants in autism spectrum disorder
ASD
Support
Excess of rare, inherited truncating mutations in autism.
ASD
Support
The landscape of somatic mutation in cerebral cortex of autistic and neurotypical individuals revealed by ultra-deep whole-genome sequencing
ASD
Support
CELF4 regulates translation and local abundance of a vast set of mRNAs, including genes associated with regulation of synaptic function.
Support
Large-Scale Exome Sequencing Study Implicates Both Developmental and Functional Changes in the Neurobiology of Autism
ASD

Rare

Variant ID
Variant Type
Allele Change
Residue Change
Inheritance Pattern
Inheritance Association
Family Type
Author, Year
 GEN487R001 
 complex_structural_alteration 
  
  
 De novo 
  
 Simplex 
 GEN487R002 
 stop_gained 
 c.493G>T 
 p.Glu165Ter 
 De novo 
  
 Simplex 
 GEN487R003 
 copy_number_loss 
  
  
 Familial 
 Maternal 
 Multi-generational 
 GEN487R004 
 stop_gained 
 c.1129C>T 
 p.Gln377Ter 
 De novo 
  
 Simplex 
 GEN487R005 
 complex_structural_alteration 
  
  
 De novo 
  
  
 GEN487R006 
 missense_variant 
 c.1120C>G 
 p.Pro374Ala 
 De novo 
  
 Multiplex 
 GEN487R007 
 missense_variant 
 c.744G>T 
 p.Met248Ile 
 De novo 
  
 Simplex 
 GEN487R008 
 intron_variant 
 c.1330+64G>A 
  
 De novo 
  
 Simplex 
 GEN487R009 
 intron_variant 
 c.1246+39C>G 
  
 De novo 
  
 Simplex 
 GEN487R010 
 missense_variant 
 ENSG00000101489:ENST00000361795:exon1:c.A29G:p.N10S,ENSG00000101489:ENST00000601392:exon1:c.A29G:p.N 
  
 De novo 
  
  
 GEN487R011 
 missense_variant 
 c.509G>T 
 p.Arg170Leu 
 Unknown 
  
  
 GEN487R012 
 missense_variant 
 c.629A>G 
 p.Asn210Ser 
 De novo 
  
  
 GEN487R013 
 missense_variant 
 c.610G>C 
 p.Glu204Gln 
 De novo 
  
 Simplex 
 GEN487R014 
 missense_variant 
 c.296T>G 
 p.Phe99Cys 
 De novo 
  
  
 GEN487R015 
 missense_variant 
 c.173T>C 
 p.Ile58Thr 
 De novo 
  
  

Common

No Common Variants Available
Chromosome
CNV Locus
CNV Type
# of studies
Animal Model
18
Duplication
 2
 
18
Duplication
 2
 
18
Deletion
 1
 
18
Deletion
 3
 
18
Deletion-Duplication
 1
 
18
Duplication
 1
 
18
Deletion-Duplication
 19
 
18
Deletion
 2
 

Model Summary

Altered excitatory neurotransmission resulting from Celf4 deficiency underlies the complex seizure disorder in Celf4 mutant mice.

References

Type
Title
Author, Year
Primary
Etiology of a genetically complex seizure disorder in Celf4 mutant mice.
Additional

M_CELF4_1_KO_HM

Model Type: Genetic
Model Genotype: Homozygous
Mutation: Celf4 gene KO with deletion of 444 bp, downstream of exon 1, using EIIA-cre in preimplantation embryos
Allele Type: Conditional loss-of-function
Strain of Origin: Not specified
Genetic Background: B6.FVB-Tg(EIIa-cre)C5379Lmgd/J
ES Cell Line: Not specified
Mutant ES Cell Line: Not Specified
Model Source: Not Specified

M_CELF4_2_KO_HM

Model Type: Genetic
Model Genotype: Homozygous
Mutation: Celf4 gene KO with deletion of 444 bp, downstream of exon1, using Meox-cre in the embryo
Allele Type: Knockout
Strain of Origin: Not specified
Genetic Background: B6.129S4-Meox2tm1(cre)Sor/J
ES Cell Line: Not specified
Mutant ES Cell Line: Not Specified
Model Source: Not Specified

M_CELF4_3_CKO_HM

Model Type: Genetic
Model Genotype: Homozygous
Mutation: Conditional deletion of 444 bp, downstream of exon 1 of Celf4 using ER-cre activated by tamoxifen in 7 week old mice
Allele Type: Conditional loss-of-function
Strain of Origin: Not specified
Genetic Background: B6.Cg-Tg(CAG-cre/Esr1*)5Amc/J
ES Cell Line: Not specified
Mutant ES Cell Line: Not Specified
Model Source: Not Specified

M_CELF4_4_CKO_HM

Model Type: Genetic
Model Genotype: Homozygous
Mutation: Conditional deletion of 444 bp, downstream of exon 1 of Celf4 using Emx1-cre, in neurons and glia of the neocortex, hippocampus and pallium, E10.5 onwards
Allele Type: Conditional loss-of-function
Strain of Origin: Not specified
Genetic Background: B6.129S2-Emx1tm1(cre)Krj/J
ES Cell Line: Not specified
Mutant ES Cell Line: Not Specified
Model Source: Not Specified

M_CELF4_5_CKO_HM

Model Type: Genetic
Model Genotype: Homozygous
Mutation: Conditional deletion of 444 bp, downstream of exon 1 of Celf4 using CamkII-cre, in excitatory neurons of the forebrain
Allele Type: Conditional loss-of-function
Strain of Origin: Not specified
Genetic Background: B6.Cg-Tg(Camk2a-cre)1Lfr/Mmcd
ES Cell Line: Not specified
Mutant ES Cell Line: Not Specified
Model Source: Not Specified

M_CELF4_6_CKO_HM_PVALBN

Model Type: Genetic
Model Genotype: Homozygous
Mutation: Conditional deletion of 444 bp, downstream of exon 1 of Celf4 using Pvalb-cre, in all parvalbumin expressing interneurons
Allele Type: Conditional loss-of-function
Strain of Origin: Not specified
Genetic Background: B6;129P2-Pvalbtm1(cre)Arbr/J
ES Cell Line: Not specified
Mutant ES Cell Line: Not Specified
Model Source: Not Specified

M_CELF4_7_CKO_HM

Model Type: Genetic
Model Genotype: Homozygous
Mutation: Conditional deletion of 444 bp, downstream of exon 1 of Celf4 using Viaat-cre, in gabaergic neurons that express Viaat- a GABA vesicular transporter
Allele Type: Conditional loss-of-function
Strain of Origin: Not specified
Genetic Background: FVB-Tg(Slc32a1-cre)/Frk
ES Cell Line: Not specified
Mutant ES Cell Line: Not Specified
Model Source: Not Specified

M_CELF4_1_KO_HM

Category
Entity
Quantity
Experimental Paradigm
Age at Testing
Seizures1
Increased
Description: Increased tonic-clonic seizures starting as early as day 21
Exp Paradigm: General observations
 General observations
 3-13 weeks
Mortality/lethality1
Increased
Description: Increased penetrance of sporadic postnatal lethality
Exp Paradigm: General observations
 General observations
 Unreported
 Not Reported: Circadian sleep/wake cycle, Communications, Emotion, Immune response, Learning & memory, Maternal behavior, Molecular profile, Motor phenotype, Neuroanatomy / ultrastructure / cytoarchitecture, Neurophysiology, Physiological parameters, Repetitive behavior, Sensory, Social behavior

M_CELF4_2_KO_HM

Category
Entity
Quantity
Experimental Paradigm
Age at Testing
Synaptic transmission: excitatory1
Increased
Description: Increased excitatory synaptic transmission indicated by higher frequency and amplitude of mepsc
Exp Paradigm: Whole cell patch clamp analysis at reverse potential of gabaergic channels in cortical layer v pyramidal neurons in the presence of tetrodotoxin
 Whole-cell patch clamp
 P14-p21
Seizures1
Increased
Description: Increased tonic-clonic seizures starting as early as day 87
Exp Paradigm: General observations
 General observations
 3-6 months
Seizures1
Increased
Description: Increased non-convulsive, or absence seizures as indicated by spike and wave discharges (swd)
Exp Paradigm: Eeg analysis
 Electroencephalogram (eeg)
 Unreported
Synaptic transmission: inhibitory1
 No change
 Whole-cell patch clamp
 P14-p21
 Not Reported: Circadian sleep/wake cycle, Communications, Developmental profile, Emotion, Immune response, Learning & memory, Maternal behavior, Molecular profile, Motor phenotype, Neuroanatomy / ultrastructure / cytoarchitecture, Physiological parameters, Repetitive behavior, Sensory, Social behavior

M_CELF4_3_CKO_HM

Category
Entity
Quantity
Experimental Paradigm
Age at Testing
Seizures1
Increased
Description: Increased seizures phenotype indicated by low electroconvulsive threshold (ect) and convulsions after routine handling
Exp Paradigm: Electroencelograph analysis
 Electroencephalogram (eeg)
 Unreported
 Not Reported: Circadian sleep/wake cycle, Communications, Developmental profile, Emotion, Immune response, Learning & memory, Maternal behavior, Molecular profile, Motor phenotype, Neuroanatomy / ultrastructure / cytoarchitecture, Neurophysiology, Physiological parameters, Repetitive behavior, Sensory, Social behavior

M_CELF4_4_CKO_HM

Category
Entity
Quantity
Experimental Paradigm
Age at Testing
Synapse density: inhibitory2
Increased
Description: The non-nuclear VGAT+Gphn+ overlapping area, which marks GABAergic synapses, was significantly increased in male mutant mice.
Exp Paradigm: VGAT, Gphn
 Immunohistochemistry
 P0
Synapse density: inhibitory2
Decreased
Description: The non-nuclear VGAT+Gphn+ overlapping area, which marks GABAergic synapses, was significantly decreased in female mutant mice.
Exp Paradigm: VGAT, Gphn
 Immunohistochemistry
 P0
Synapse density: excitatory2
Increased
Description: The vGlut2+ PSD95+ overlapping area, which labels glutamatergic synapses, was significantly increased in the subplate of male mutant mice.
Exp Paradigm: VGlut1, VGlut2, PSD95
 Immunohistochemistry
 P0
Neuronal number: excitatory neurons1
Decreased
Description: Decreased number of celf4-staining excitatory neurons in cerebral cortex and hippocampus
Exp Paradigm: Immunohistochemical analysis
 Immunohistochemistry
 Unreported
Seizures1
Increased
Description: Increased seizures phenotype indicated by low electroconvulsive threshold (ect) and convulsions after routine handling
Exp Paradigm: Electroencelograph analysis
 Electroencephalogram (eeg)
 Unreported
Regulation of translation2
Abnormal
Description: Isoform-level differential expression analysis of monosome and polysome fractions reveals 729 isoform mRNAs with differences in association with monosome, 239 isoform mRNAs predominantly associated only with translating polysomes, and 89 isoforms with changes in association with both monosomes and polysomes. In isoform mRNAs with differential association with polysomes, 145 and 183 mRNA isoforms were translationally derepressed and repressed, respectively.
 Polysome profiling
 P0
Targeted expression2
Decreased
Description: Celf4 conditional knockout shows a loss of Celf4 protein in whole neocortex.
Exp Paradigm: Celf4
 Western blot
 P0
Protein localization: synapse2
Increased
Description: Sv2/Sv2a protein levels are significantly increased in mutant synaptoneurosomes.
Exp Paradigm: Sv2 in synaptoneurosomes
 Western blot
 P0
Targeted expression2
Decreased
Description: Celf4 conditional knockout shows a loss of Celf4 protein in the subplate and cortical layers.
Exp Paradigm: Celf4
 Immunohistochemistry
 P0
Protein expression: in situ protein expression2
Abnormal
Description: Eif4a2 protein expression was evidently reduced while the Sv2a protein punctate staining was increased in the subplate of Celf4 mutants. Protein expression from Syp mRNAs was also increased in the subplate of the Celf4 conditional knockout mouse neocortex.
Exp Paradigm: Eif4a2, Sv2a, Syp
 Immunohistochemistry
 P0
Regulation of translation2
Abnormal
Description: To confirm whether transcripts identified in the polysome profiling-RNA seq analysis are subjected to translational regulation, relative mRNA levels (polysome/monosome ratio) were measured via qRT-PCR on previously sequenced sucrose gradient fractions. Several synaptic mRNAs (Homer2, Sema4c, Ank2, Srcin1), including Celf4 targets (Map1b, Ppp1r9a, Sv2a, Syp, and Slc17a7/vGlut1) had a significantly greater polysome/monosome ratio, suggesting their distribution is shifted to polysomal fractions in conditional knockouts. The mRNA level of Celf4 target Eif4a2 was strongly decreased in polysome/monosome ratio, implying that Eif4a2 mRNA is predominantly associated with monosomes when Celf4 is knocked out.
 Quantitative PCR (qRT-PCR)
 P0
Gene expression2
 No change
 Quantitative PCR (qRT-PCR)
 P0
Protein expression level evidence2
 No change
 Western blot
 P0
Cortical lamination2
 No change
 Immunohistochemistry
 P0
Neuronal number: inhibitory neurons1
 No change
 Immunohistochemistry
 Unreported
Synapse density: excitatory2
 No change
 Immunohistochemistry
 P0
 Not Reported: Circadian sleep/wake cycle, Communications, Developmental profile, Emotion, Immune response, Learning & memory, Maternal behavior, Molecular profile, Motor phenotype, Neurophysiology, Physiological parameters, Repetitive behavior, Sensory, Social behavior

M_CELF4_5_CKO_HM

Category
Entity
Quantity
Experimental Paradigm
Age at Testing
Seizures1
Increased
Description: Increased seizures phenotype indicated by low electroconvulsive threshold (ect) and convulsions after routine handling
Exp Paradigm: Electroencelograph analysis
 Electroencephalogram (eeg)
 Unreported
 Not Reported: Circadian sleep/wake cycle, Communications, Developmental profile, Emotion, Immune response, Learning & memory, Maternal behavior, Molecular profile, Motor phenotype, Neuroanatomy / ultrastructure / cytoarchitecture, Neurophysiology, Physiological parameters, Repetitive behavior, Sensory, Social behavior

M_CELF4_6_CKO_HM_PVALBN

Category
Entity
Quantity
Experimental Paradigm
Age at Testing
Seizures1
 No change
 Electroencephalogram (eeg)
 Unreported
 Not Reported: Circadian sleep/wake cycle, Communications, Developmental profile, Emotion, Immune response, Learning & memory, Maternal behavior, Molecular profile, Motor phenotype, Neuroanatomy / ultrastructure / cytoarchitecture, Neurophysiology, Physiological parameters, Repetitive behavior, Sensory, Social behavior

M_CELF4_7_CKO_HM

Category
Entity
Quantity
Experimental Paradigm
Age at Testing
Seizures1
 No change
 Electroencephalogram (eeg)
 Unreported
 Not Reported: Circadian sleep/wake cycle, Communications, Developmental profile, Emotion, Immune response, Learning & memory, Maternal behavior, Molecular profile, Motor phenotype, Neuroanatomy / ultrastructure / cytoarchitecture, Neurophysiology, Physiological parameters, Repetitive behavior, Sensory, Social behavior

 

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