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Relevance to Autism

Three different homozygous variants (one nonsense, one frameshift, one missense) in the BCKDK gene that segregated with disease were identified in three consanguineous families presenting with autism and ID (Novarino et al., 2012).

Molecular Function

Catalyzes the phosphorylation and inactivation of the branched-chain alpha-ketoacid dehydrogenase complex, the key regulatory enzyme of the valine, leucine and isoleucine catabolic pathways. Key enzyme that regulate the activity state of the BCKD complex. Defects in this gene are associated with branched-chain ketoacid dehydrogenase kinase deficiency (BCKDKD) [MIM:614923], a metabolic disorder characterized by autism, epilepsy, intellectual disability, and reduced branched-chain amino acids.

External Links

        

References

Type
Title
Type of Disorder
Associated Disorders
Author, Year
Primary
Mutations in BCKD-kinase lead to a potentially treatable form of autism with epilepsy.
Branched-chain ketoacid dehydrogenase kinase defic
ASD, ID, epilepsy
Support
Inherited and De Novo Genetic Risk for Autism Impacts Shared Networks.
ASD
Support
Whole genome sequencing analysis identifies sex differences of familial pattern contributing to phenotypic diversity in autism
ASD
Support
Integrating de novo and inherited variants in 42
ASD
Support
Novel Loss of Function Variant in BCKDK Causes a Treatable Developmental and Epileptic Encephalopathy
ASD, DD, epilepsy/seizures
Support
Genome sequencing of 320 Chinese children with epilepsy: a clinical and molecular study
ASD, DD, epilepsy/seizures
Recent Recommendation
Two novel mutations in the BCKDK (branched-chain keto-acid dehydrogenase kinase) gene are responsible for a neurobehavioral deficit in two pediatri...
Branched-chain ketoacid dehydrogenase kinase defic
DD
Recent Recommendation
Structure-based design and mechanisms of allosteric inhibitors for mitochondrial branched-chain -ketoacid dehydrogenase kinase.
Recent Recommendation
ASD, DD, ID
Epilepsy/seizures
Variant ID
Variant Type
Allele Change
Residue Change
Inheritance Pattern
Inheritance Association
Family Type
Author, Year
 GEN423R001a 
 stop_gained 
 c.466C>T 
 p.Arg156Ter 
 Familial 
 Both parents 
 Multiplex 
 GEN423R002a 
 frameshift_variant 
 c.222del 
 p.Met74IlefsTer15 
 Familial 
 Both parents 
 Multiplex 
 GEN423R003a 
 missense_variant 
 c.671G>C 
 p.Arg224Pro 
 Familial 
 Both parents 
 Multiplex 
 GEN423R004a 
 splice_site_variant 
 c.520C>G 
 p.Arg174Gly 
 Familial 
 Both parents 
 Simplex 
 GEN423R005a 
 missense_variant 
 c.1166T>C 
 p.Leu389Pro 
 Familial 
 Both parents 
 Simplex 
 GEN423R006 
 frameshift_variant 
 c.986dup 
 p.Met329IlefsTer9 
 Familial 
 Maternal 
 Multiplex 
 GEN423R007a 
 frameshift_variant 
 c.159_160dup 
 p.Tyr54PhefsTer18 
 Familial 
 Maternal 
  
 GEN423R007b 
 splice_site_variant 
 c.716+1G>A 
  
 Familial 
 Paternal 
  
 GEN423R008a 
 inframe_deletion 
 c.999_1001del 
 p.Thr335del 
 Familial 
 Both parents 
 Multiplex 
 GEN423R009 
 missense_variant 
 c.256C>T 
 p.His86Tyr 
 De novo 
  
  
 GEN423R010a 
 stop_gained 
 c.466C>T 
 p.Arg156Ter 
 Familial 
 Both parents 
 Multiplex 
 GEN423R011a 
 stop_gained 
 c.466C>T 
 p.Arg156Ter 
 Familial 
 Both parents 
 Multiplex 
 GEN423R012a 
 stop_gained 
 c.466C>T 
 p.Arg156Ter 
 Familial 
 Both parents 
 Multiplex 
 GEN423R013a 
 stop_gained 
 c.1159C>T 
 p.Gln387Ter 
 Familial 
 Both parents 
 Simplex 
 GEN423R014a 
 stop_gained 
 c.14C>A 
 p.Ser5Ter 
 Familial 
 Both parents 
 Simplex 
 GEN423R015a 
 splice_site_variant 
 c.265-2A>G 
  
 Familial 
 Both parents 
 Simplex 
 GEN423R016a 
 splice_site_variant 
 c.264+1G>C 
  
 Familial 
 Both parents 
 Multiplex 
 GEN423R017a 
 stop_gained 
 c.433C>T 
 p.Gln145Ter 
 Unknown 
  
 Simplex 
 GEN423R017b 
 missense_variant 
 c.1100G>A 
 p.Gly367Asp 
 Unknown 
  
 Simplex 
 GEN423R018a 
 stop_gained 
 c.466C>T 
 p.Arg156Ter 
 Familial 
 Both parents 
 Multiplex 
 GEN423R019a 
 missense_variant 
 c.617A>C 
 p.His206Pro 
 Familial 
 Both parents 
 Simplex 
 GEN423R020 
 missense_variant 
 c.1216C>T 
 p.Arg406Trp 
 De novo 
  
  
Chromosome
CNV Locus
CNV Type
# of studies
Animal Model
16
Deletion-Duplication
 150
  construct
16
Deletion
 1
 
16
Deletion
 1
 

Model Summary

Bckdk null mice have lower blood and tissue levels of the BCAAs. The mutant mice are 15% smaller at 12 weeks and the brain, muscle and adipose tissue weights are reduced, whereas weights of the liver and kidney are greater. Hind limb flexion is observed in the mutant mice throughout life and epileptic seizures start after 6-7 months of age. Bckdk null mice show significant improvement in growth and appearance when fed a high protein diet or BCAA-enriched diet. Bckdk nulls also exhibit defects in motor related tests, social interactions, and abnormal neurotransmission in layer 2/3 of the somatosensory cortex and cerebellar Purkinje cells.

References

Type
Title
Author, Year
Primary
Impaired growth and neurological abnormalities in branched-chain alpha-keto acid dehydrogenase kinase-deficient mice.
Primary
Mutations in BCKD-kinase lead to a potentially treatable form of autism with epilepsy.
Primary
Impaired Amino Acid Transport at the Blood Brain Barrier Is a Cause of Autism Spectrum Disorder.
Model Type: Genetic
Model Genotype: Homozygous
Mutation: Bckdk gene was disrupted with a gene trap vector, upstream of exon2.
Allele Type: Targeted (Knock Out)
Strain of Origin: Not specified
Genetic Background: C57BL/6J
ES Cell Line: 129/SvEvBrd
Mutant ES Cell Line: Not specified
Model Source: Not specified
Category
Entity
Quantity
Experimental Paradigm
Age at Testing
Limb posture2
Decreased
 Tail suspension test
 NA
Gait1
Decreased
 General observations
 3 weeks
Limb posture1
Decreased
 Tail suspension test
 NA
General locomotor activity3
Decreased
 Open field test
 P55-p65
Motor coordination and balance3
Decreased
 Balance beam test
 P55-p65
Gait3
Decreased
 Gait
 P55-p65
Brain size1
Decreased
 Histology
 NA
Miniature post synaptic current amplitude: excitatory3
Increased
 Whole-cell patch clamp
 P21
Miniature post synaptic current frequency: inhibitory3
Decreased
 Whole-cell patch clamp
 P21
Seizures1
Increased
 Observation of seizures
 6-7 months
Seizures2
Increased
 Observation of seizures
 NA
Social approach3
Decreased
 Three-chamber social approach test
 P55-p65
Rearing behavior3
Decreased
 Open field test
 P55-p65
Reproductive function1
Decreased
 General observations
 Adult
Metabolic function1
Increased
 Measurement of valine utilization
 NA
Developmental trajectory1
Decreased
 General observations
 4-6 weeks
Tissue weight1
Increased
 Measurement of tissue weight
 NA
Tissue weight1
Decreased
 Measurement of tissue weight
 NA
Size/growth1
Decreased
 General observations
 2-3 weeks
Amino acid levels1
Decreased
 Ion-exchange chromatography
 NA
Protein phosphorylation2
Decreased
 Western blot
 NA
Enzyme activity1
Increased
 Spectrophotometry
 Unreported
Protein phosphorylation1
Decreased
 Western blot
 NA
Amino acid levels2
Increased
 High-performance liquid chromatography (hplc)
 P14
Targeted expression1
Decreased
 Western blot
 NA
Protein expression level evidence1
Increased
 Western blot
 NA
Amino acid levels2
Decreased
 High-performance liquid chromatography (hplc)
 P14
Protein phosphorylation1
Increased
 Western blot
 NA
Gene expression2
Increased
 Gene expression microarray
 NA
Mortality/lethality1
 No change
 Genotypic ratio of progeny from heterozygous parents
 Unreported
Tissue weight1
 No change
 Measurement of tissue weight
 NA
Amino acid levels1
 No change
 Ion-exchange chromatography
 NA
Protein expression level evidence1
 No change
 Western blot
 NA
Protein expression level evidence1
 No change
 Western blot
 NA
Brain morphology1
 No change
 Histology
 NA
Brain morphology2
 No change
 Histology
 NA
Cortical lamination2
 No change
 Immunostaining
 NA
Miniature post synaptic current amplitude: inhibitory3
 No change
 Whole-cell patch clamp
 P21
Miniature post synaptic current frequency: excitatory3
 No change
 Whole-cell patch clamp
 P21
Neurotransmitter release3
 No change
 Liquid chromatography-mass spectrometry (lc-ms)
 P2-p40
 Not Reported: Circadian sleep/wake cycle, Communications, Developmental profile, Emotion, Immune response, Learning & memory, Maternal behavior, Molecular profile, Neuroanatomy / ultrastructure / cytoarchitecture, Neurophysiology, Physiological parameters, Repetitive behavior, Seizure, Sensory, Social behavior


Interactor Symbol Interactor Name Interactor Organism Entrez ID Uniprot ID Interaction Type Evidence Reference
BCKDHA branched chain keto acid dehydrogenase E1, alpha polypeptide 593 B4DP47 IP; MS
Ewing RM , et al. 2007
CAB39 calcium binding protein 39 51719 A8K8L7 IP; MS
Ewing RM , et al. 2007
CAB39L calcium binding protein 39-like 81617 Q9H9S4 IP; MS
Ewing RM , et al. 2007
CETN1 Centrin-1 1068 Q12798 IP; LC-MS/MS
Huttlin EL , et al. 2015
CETN2 centrin, EF-hand protein, 2 1069 P41208 IP; LC-MS/MS
Huttlin EL , et al. 2015
CETN3 centrin, EF-hand protein, 3 1070 O15182 IP; LC-MS/MS
Huttlin EL , et al. 2015
CHD2 chromodomain helicase DNA binding protein 2 1106 O14647 LC-MS/MS
Vertegaal AC , et al. 2006
FAM98B family with sequence similarity 98, member B 283742 Q52LJ0 IP; MS
Ewing RM , et al. 2007
FMR1 fragile X mental retardation 1 2332 G8JLE9 PAR-CLIP
Ascano M Jr , et al. 2012
GCNT3 Beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase 3 9245 O95395 IP; LC-MS/MS
Huttlin EL , et al. 2015
ISLR Immunoglobulin superfamily containing leucine-rich repeat protein 3671 O14498 IP; LC-MS/MS
Huttlin EL , et al. 2015
LGALS3BP lectin, galactoside-binding, soluble, 3 binding protein 3959 Q08380 IP; LC-MS/MS
Huttlin EL , et al. 2015
METTL21C Protein-lysine methyltransferase METTL21C 196541 Q5VZV1 IP; LC-MS/MS
Huttlin EL , et al. 2015
MRPL12 mitochondrial ribosomal protein L12 6182 P52815 IP; LC-MS/MS
Huttlin EL , et al. 2015
NBEA neurobeachin 26422 Q9EPN1 Y2H
Tuand K , et al. 2016
NIT1 nitrilase 1 NM_005600 Q86X76 IP; LC-MS/MS
Huttlin EL , et al. 2015
RNF219 ring finger protein 219 79596 Q5W0B1 IP; MS
Ewing RM , et al. 2007
RTCA RNA 3'-terminal phosphate cyclase 8634 O00442 IP; MS
Ewing RM , et al. 2007
TERF2 telomeric repeat binding factor 2 7014 Q9NYB0 MudPIT; LC-MS/MS
Giannone RJ , et al. 2010
TRAF4 TNF receptor-associated factor 4 9618 Q9BUZ4 Y2H
Xu YC , et al. 2002
UBC ubiquitin C 7316 P63279 IP; MS
Wagner SA , et al. 2011
UBE3A ubiquitin protein ligase E3A 7337 Q05086 IP; MS; COMPASS
Martnez-Nol G , et al. 2012
WDTC1 WD and tetratricopeptide repeats 1 23038 Q8N5D0 IP; LC-MS/MS
Huttlin EL , et al. 2015

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