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Relevance to Autism

Variants in the KCNT1 gene co-segregated with disease in three families with autosomal dominant nocturnal frontal lobe epilepsy (ADNFLE) with major comorbidites of intellectual disability and psychiatric features (Heron et al., 2012). Furthermore, de novo variants in KCNT1 were identified in sporadic cases with nocturnal frontal lobe epilepsy (NFLE) and malignant migrating partial seizures of infancy (MMPSI) (Heron et al., 2012; Barcia et al., 2012). FMRP, the protein encoded by the syndromic ASD gene FMR1, binds to the C-terminus of the potassium channel encoded by KCNT1 to activate the channel (PMID 20512134).

Molecular Function

Potassium channels represent the most complex class of voltage-gated ion channels from both functional and structural standpoints. Their diverse functions include regulating neurotransmitter release, heart rate, insulin secretion, neuronal excitability, epithelial electrolyte transport, smooth muscle contraction, and cell volume. This gene encodes a sodium-activated potassium channel subunit which is thought to function in ion conductance and developmental signaling pathways. Mutations in this gene cause the early-onset epileptic disorders, malignant migrating partial seizures of infancy and autosomal dominant nocturnal frontal lobe epilepsy.

External Links

        

References

Type
Title
Type of Disorder
Associated Disorders
Author, Year
Primary
Missense mutations in the sodium-gated potassium channel gene KCNT1 cause severe autosomal dominant nocturnal frontal lobe epilepsy.
Epilepsy
ID
Positive Association
De novo mutations in epileptic encephalopathies.
Epilepsy
IS, LGS, DD, ID, ASD, ADHD
Support
Genetic analysis using targeted exome sequencing of 53 Vietnamese children with developmental and epileptic encephalopathies
DD, epilepsy/seizures
Support
Exome sequencing of ion channel genes reveals complex profiles confounding personal risk assessment in epilepsy.
Epilepsy
Support
DD, epilepsy/seizures
Support
High Rate of Recurrent De Novo Mutations in Developmental and Epileptic Encephalopathies.
Epilepsy/seizures
DD/ID
Support
A single center experience with publicly funded clinical exome sequencing for neurodevelopmental disorders or multiple congenital anomalies
DD, ID, epilepsy/seizures
Support
Epilepsy/seizures
DD
Support
Genomic diagnosis for children with intellectual disability and/or developmental delay.
ASD, ID, epilepsy/seizures
Support
Genome sequencing of 320 Chinese children with epilepsy: a clinical and molecular study
DD, epilepsy/seizures
Support
ID, epilepsy/seizures
Support
Diagnostic Targeted Resequencing in 349 Patients with Drug-Resistant Pediatric Epilepsies Identifies Causative Mutations in 30 Different Genes.
Epilepsy/seizures
Microcephaly
Support
De novo variants in neurodevelopmental disorders-experiences from a tertiary care center
DD, epilepsy/seizures
Support
ASD
DD, ID, epilepsy/seizures
Support
High diagnostic yield of syndromic intellectual disability by targeted next-generation sequencing.
ID, epilepsy/seizures
Support
A recurrent PJA1 variant in trigonocephaly and neurodevelopmental disorders
ID, epilepsy/seizures
Support
Integrating de novo and inherited variants in 42
ASD
Support
Targeted resequencing in epileptic encephalopathies identifies de novo mutations in CHD2 and SYNGAP1.
Epilepsy
ID, ASD, DD
Support
Phenotype-to-genotype approach reveals head-circumference-associated genes in an autism spectrum disorder cohort.
ASD
Macrocephaly
Support
Genetic and Phenotype Analysis of a Chinese Cohort of Infants and Children With Epilepsy
Epilepsy/seizures
Support
De novo gain-of-function KCNT1 channel mutations cause malignant migrating partial seizures of infancy.
Epilepsy
Support
The combination of whole-exome sequencing and copy number variation sequencing enables the diagnosis of rare neurological disorders.
Epilepsy/seizures
DD, ID
Recent Recommendation
Fragile X mental retardation protein controls gating of the sodium-activated potassium channel Slack.

Rare

Variant ID
Variant Type
Allele Change
Residue Change
Inheritance Pattern
Inheritance Association
Family Type
Author, Year
 GEN434R001a 
 missense_variant 
 c.2782C>T 
 p.Arg928Cys 
 Familial 
 Maternal and Paternal 
 Multi-generational 
 GEN434R002a 
 missense_variant 
 c.2386T>C 
 p.Tyr796His 
 Familial 
 Maternal and Paternal 
 Multi-generational 
 GEN434R003 
 missense_variant 
 c.1193G>A 
 p.Arg398Gln 
 Familial 
 Paternal 
 Multiplex 
 GEN434R004 
 missense_variant 
 c.2688G>A 
 p.Met896Ile 
 De novo 
  
 Simplex 
 GEN434R005 
 missense_variant 
 c.1283G>A 
 p.Arg428Gln 
 De novo 
  
 Simplex 
 GEN434R006 
 missense_variant 
 c.1421G>A 
 p.Arg474His 
 De novo 
  
 Simplex 
 GEN434R007 
 missense_variant 
 c.2280C>G 
 p.Ile760Met 
 De novo 
  
 Simplex 
 GEN434R008 
 missense_variant 
 c.2800G>A 
 p.Ala934Thr 
 De novo 
  
 Simplex 
 GEN434R009 
 synonymous_variant 
 c.2430C>T 
 p.Ala810= 
 Unknown 
  
 Unknown 
 GEN434R010 
 synonymous_variant 
 c.2376C>T 
 p.Asp792= 
 Unknown 
  
 Unknown 
 GEN434R011 
 missense_variant 
 c.2756C>T 
 p.Thr919Met 
 Unknown 
  
 Unknown 
 GEN434R012 
 stop_gained 
 c.1330C>T 
 p.Arg444Ter 
 Unknown 
  
 Unknown 
 GEN434R013 
 missense_variant 
 c.3341G>A 
 p.Arg1114Gln 
 Unknown 
  
  
 GEN434R014 
 missense_variant 
 c.3158C>A 
 p.Pro1053His 
 Unknown 
  
  
 GEN434R015 
 missense_variant 
 c.1742C>T 
 p.Thr581Ile 
 Unknown 
  
  
 GEN434R016 
 missense_variant 
 c.2771C>T 
 p.Pro924Leu 
 De novo 
  
  
 GEN434R017 
 missense_variant 
 c.2800G>A 
 p.Ala934Thr 
 De novo 
  
  
 GEN434R018 
 missense_variant 
 c.2839A>G 
 p.Lys947Glu 
 De novo 
  
  
 GEN434R019 
 missense_variant 
 c.1546A>G 
 p.Met516Val 
 Unknown 
  
  
 GEN434R020a 
 missense_variant 
 c.136C>T 
 p.Leu46Phe 
  
  
  
 GEN434R020b 
 missense_variant 
 c.2729G>A 
 p.Arg910Gln 
  
  
  
 GEN434R021 
 missense_variant 
 c.2714G>A 
 p.Arg905Gln 
 De novo 
  
 Simplex 
 GEN434R022 
 missense_variant 
 c.2665G>A 
 p.Ala889Thr 
 De novo 
  
 Simplex 
 GEN434R023 
 missense_variant 
 c.641G>A 
 p.Arg214Gln 
 De novo 
  
 Simplex 
 GEN434R024 
 missense_variant 
 c.1420C>T 
 p.Arg474Cys 
 De novo 
  
  
 GEN434R025 
 frameshift_variant 
 c.20del 
 p.Ala7GlyfsTer59 
 Familial 
 Paternal 
 Simplex 
 GEN434R026 
 missense_variant 
 c.2870C>A 
 p.Ala957Asp 
 De novo 
  
 Simplex 
 GEN434R027 
 missense_variant 
 c.1283G>A 
 p.Arg428Gln 
 De novo 
  
 Unknown 
 GEN434R028 
 missense_variant 
 c.1750A>G 
 p.Lys584Glu 
 Unknown 
  
  
 GEN434R029 
 missense_variant 
 c.1421G>A 
 p.Arg474His 
 De novo 
  
 Simplex 
 GEN434R030 
 missense_variant 
 c.1421G>A 
 p.Arg474His 
 De novo 
  
 Simplex 
 GEN434R031 
 missense_variant 
 c.1421G>A 
 p.Arg474His 
 De novo 
  
  
 GEN434R032 
 missense_variant 
 c.2690C>T 
 p.Ala897Val 
 Unknown 
  
  
 GEN434R033 
 frameshift_variant 
 c.108del 
 p.Arg37GlyfsTer18 
 De novo 
  
  
 GEN434R034 
 missense_variant 
 c.303C>A 
 p.Leu101%3D 
 De novo 
  
 Simplex 
 GEN434R035 
 missense_variant 
 c.1916C>T 
 p.Thr639Met 
 De novo 
  
  
 GEN434R036 
 frameshift_variant 
 c.2093_2094del 
 p.Pro698HisfsTer37 
 De novo 
  
  
 GEN434R037 
 missense_variant 
 c.2656G>A 
 p.Glu886Lys 
 De novo 
  
  
 GEN434R038 
 synonymous_variant 
 c.3489C>T 
 p.Pro1163%3D 
 De novo 
  
  
 GEN434R039 
 splice_region_variant 
 c.615+3A>G 
  
 Familial 
 Maternal 
 Simplex 
 GEN434R040 
 missense_variant 
 c.862G>A 
 p.Gly288Ser 
 Familial 
 Paternal 
 Multiplex 
  et al.  
 GEN434R041 
 missense_variant 
 c.3001A>T 
 p.Thr1001Ser 
 De novo 
  
  
  et al.  
 GEN434R042 
 missense_variant 
 c.1546A>G 
 p.Met516Val 
 De novo 
  
  
  et al.  
 GEN434R043 
 missense_variant 
 c.2800G>A 
 p.Ala934Thr 
 Unknown 
  
  
  et al.  

Common

No Common Variants Available
Chromosome
CNV Locus
CNV Type
# of studies
Animal Model
9
Duplication
 1
 
9
Deletion
 1
 
9
Duplication
 1
 
9
Duplication
 1
 
9
Duplication
 2
 
9
Deletion-Duplication
 9
 
9
Deletion-Duplication
 45
 

No Animal Model Data Available


Interactor Symbol Interactor Name Interactor Organism Entrez ID Uniprot ID Interaction Type Evidence Reference
KCNT1 potassium channel, subfamily T, member 1 395248 Q8QFV0 Cryo-electron microscopy
Hite RK , et al. 2015
FMR1 fragile X mental retardation 1 14265 P35922 Y2H; IP/WB
Brown MR , et al. 2010
KCNT1 potassium channel, subfamily T, member 1 57582 Q5JUK3 Cryo-electron microscopy
Hite RK , et al. 2015

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