Summary Statistics:
ASD Reports: 23
Recent Reports: 1
Annotated variants: 44
Associated CNVs: 7
Evidence score: 2
Gene Score: 5
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.
References
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.
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
GEN434R041
missense_variant
c.3001A>T
p.Thr1001Ser
De novo
GEN434R042
missense_variant
c.1546A>G
p.Met516Val
De novo
GEN434R043
missense_variant
c.2800G>A
p.Ala934Thr
Unknown
No Common Variants Available
9
Deletion-Duplication
45
No Animal Model Data Available
Summary Statistics:
Total Interactions: 3
Total Publications: 2
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