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Relevance to Autism

Systematic investigation of the phenotypic and molecular genetic data of 1,577 patients from the TRANSLATE NAMSE cohort who had undergone exome sequencing and were partially analyzed with next-generation phenotypic approaches in Schmidt et al., 2024 identified a de novo missense variant in the KCNN2 gene in an adult female.with autism and specific learning disability. A de novo missense variant that was predicted to be deleterious and a de novo nonsense variant in KCNN2 have recently been reported in ASD probands (Zhou et al., 2022; Fu et al., 2022). Mochel et al., 2020 described individuals with KCNN2-associated neurodevelopmental disorder, which was characterized by developmental delay, intellectual disability, behavioral disturbances, and movement disorders; two out of 10 of these individuals were reported to have autism spectrum disorder, while autistic features were reported in four other cases. Subsequent functional assessment of six variants identified in affected individuals in this report by patch-clamp electrophysiology found that five resulted in loss-of-function effects.

Molecular Function

Action potentials in vertebrate neurons are followed by an afterhyperpolarization (AHP) that may persist for several seconds and may have profound consequences for the firing pattern of the neuron. Each component of the AHP is kinetically distinct and is mediated by different calcium-activated potassium channels. The protein encoded by this gene is activated before membrane hyperpolarization and is thought to regulate neuronal excitability by contributing to the slow component of synaptic AHP. This gene is a member of the KCNN family of potassium channel genes. The encoded protein is an integral membrane protein that forms a voltage-independent calcium-activated channel with three other calmodulin-binding subunits.

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References

Type
Title
Type of Disorder
Associated Disorders
Author, Year
Primary
Next-generation phenotyping integrated in a national framework for patients with ultrarare disorders improves genetic diagnostics and yields new molecular findings
ASD
Learning disability
Support
Variants in the SK2 channel gene (KCNN2) lead to dominant neurodevelopmental movement disorders
DD, ID
ASD or autistic features, ADHD, epilepsy/seizures
Support
Genomic reanalysis of a pan-European rare-disease resource yields new diagnoses
ASD, DD
Support
Rare coding variation provides insight into the genetic architecture and phenotypic context of autism
ASD
Support
Integrating de novo and inherited variants in 42
ASD

Rare

Variant ID
Variant Type
Allele Change
Residue Change
Inheritance Pattern
Inheritance Association
Family Type
Author, Year
 GEN1461R001 
 missense_variant 
 c.863T>C 
 p.Ile288Thr 
 De novo 
  
  
 GEN1461R002 
 missense_variant 
 c.965G>C 
 p.Trp322Ser 
 De novo 
  
  
 GEN1461R003 
 stop_gained 
 c.480C>A 
 p.Tyr160Ter 
 De novo 
  
  
 GEN1461R004 
 stop_gained 
 c.800_803del 
 p.Tyr267Ter 
 De novo 
  
  
 GEN1461R005 
 stop_gained 
 c.480C>A 
 p.Tyr160Ter 
 De novo 
  
  
 GEN1461R006 
 missense_variant 
 c.862_863delinsTC 
 p.Ile288Ser 
 De novo 
  
  
 GEN1461R007 
 inframe_deletion 
 c.962_964delTAT 
 p.Leu321del 
 De novo 
  
  
 GEN1461R008 
 missense_variant 
 c.1077 T>G 
 p.Ile359Met 
 De novo 
  
  
 GEN1461R009 
 missense_variant 
 c.1082A>G 
 p.Tyr361Cys 
 De novo 
  
  
 GEN1461R010 
 missense_variant 
 c.1084G>A 
 p.Gly362Ser 
 De novo 
  
  
 GEN1461R011 
 missense_variant 
 c.1162C>G 
 p.Leu388Val 
 De novo 
  
  
 GEN1461R012 
 splice_site_variant 
 c.1254+2T>C 
  
 De novo 
  
  
 GEN1461R013 
 missense_variant 
 c.1295T>C 
 p.Leu432Pro 
 Familial 
 Maternal 
  
 GEN1461R014 
 missense_variant 
 c.88G>C 
 p.Glu30Gln 
 De novo 
  
  
 GEN1461R015 
 stop_gained 
 c.480C>A 
 p.Tyr160Ter 
 De novo 
  
 Simplex 

Common

No Common Variants Available
Chromosome
CNV Locus
CNV Type
# of studies
Animal Model
5
Duplication
 1
 
5
Deletion
 1
 
5
Deletion
 1
 
5
Deletion-Duplication
 14
 
5
Deletion
 8
 
5
Duplication
 1
 

No Animal Model Data Available

No PIN Data Available
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