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Relevance to Autism

Functionally-impairing missense variants in the SLC12A5 previously observed in epilepsy cases were identified in probands from a Quebec ASD cohort. Subsequent analysis of a combined dataset indicated that there was an enrichment of coding variants in the target region of the C-terminus of KCC2 in ASD cases compared to controls (P=0.03); this statistically significant enrichment increased when considering variants in this region that either disrupted or introduced a CpG site (P=6.8E-03) (Merner et al., 2015).

Molecular Function

This gene encodes an integral membrane K-Cl cotransporter that mediates electroneutral potassium-chloride cotransport in mature neurons and is important for Cl-homeostasis in neurons. Mutations in this gene have been associated with febrile seizures (Puskarjov et al., 2014), idiopathic generalized epilepsy (Kahle et al., 2014), and epilepsy of infancy with migrating focal seizures (Stodberg et al., 2015).

External Links

        

References

Type
Title
Type of Disorder
Associated Disorders
Author, Year
Primary
Regulatory domain or CpG site variation in SLC12A5, encoding the chloride transporter KCC2, in human autism and schizophrenia.
ASD
SCZ
Support
Genetically encoded impairment of neuronal KCC2 cotransporter function in human idiopathic generalized epilepsy.
Epilepsy/seizures
Support
Integrating de novo and inherited variants in 42
ASD
Support
A variant of KCC2 from patients with febrile seizures impairs neuronal Cl- extrusion and dendritic spine formation.
Epilepsy/seizures
Support
2022
TS
Support
Disruption of KCC2 in Parvalbumin-Positive Interneurons Is Associated With a Decreased Seizure Threshold and a Progressive Loss of Parvalbumin-Positive Interneurons
Epilepsy/seizures
Support
The landscape of somatic mutation in cerebral cortex of autistic and neurotypical individuals revealed by ultra-deep whole-genome sequencing
ASD
Support
Exonic Mosaic Mutations Contribute Risk for Autism Spectrum Disorder.
ASD
Support
Mutations in SLC12A5 in epilepsy of infancy with migrating focal seizures.
Epilepsy/seizures

Rare

Variant ID
Variant Type
Allele Change
Residue Change
Inheritance Pattern
Inheritance Association
Family Type
Author, Year
 GEN783R001 
 missense_variant 
 c.2855G>A,c.2924G>A 
 p.Arg952His, p.Arg975His 
 Unknown 
  
  
 GEN783R002 
 synonymous_variant 
 c.3030G>A 
 p.Pro1010= 
 Unknown 
  
  
 GEN783R003 
 missense_variant 
 c.3211C>T 
 p.Arg1071Trp 
 Unknown 
  
  
 GEN783R004 
 missense_variant 
 c.3214C>T 
 p.Arg1072Cys 
 Unknown 
  
  
 GEN783R005 
 missense_variant 
 c.2924G>A 
 p.Arg975His 
 Unknown 
  
  
 GEN783R006 
 synonymous_variant 
 c.2874T>C 
 p.Asp958= 
 Unknown 
  
  
 GEN783R007 
 missense_variant 
 c.2924G>A 
 p.Arg975His 
 Familial 
 Paternal 
 Simplex 
 GEN783R008 
 missense_variant 
 c.2924G>A 
 p.Arg975His 
 Unknown 
  
  
 GEN783R009 
 missense_variant 
 c.3214C>T 
 p.Arg1072Cys 
 Unknown 
  
  
 GEN783R010a 
 missense_variant 
 c.1277T>C 
 p.Leu426Pro 
 Familial 
  
 Multiplex 
 GEN783R010b 
 missense_variant 
 c.1652G>A 
 p.Gly551Asp 
 Familial 
  
 Multiplex 
 GEN783R011a 
 missense_variant 
 c.932T>A 
 p.Leu311His 
 Familial 
 Both parents 
 Multiplex 
 GEN783R012 
 missense_variant 
 c.2548G>A 
 p.Asp850Asn 
 De novo 
  
 Simplex 
 GEN783R013 
 missense_variant 
 ENSG00000124140:ENST00000243964:exon21:c.G2735A:p.R912H,ENSG00000124140:ENST00000454036:exon21:c.G28 
  
 De novo 
  
  
 GEN783R014 
 missense_variant 
 c.923C>T 
 p.Pro308Leu 
 De novo 
  
  
 GEN783R015 
 missense_variant 
 c.1079G>A 
 p.Arg360Gln 
 De novo 
  
  
 GEN783R016 
 missense_variant 
 c.2276A>C 
 p.Glu759Ala 
 De novo 
  
  
 GEN783R017 
 stop_gained 
 c.1936C>T 
 p.Leu646Phe 
 De novo 
  
  

Common

No Common Variants Available
Chromosome
CNV Locus
CNV Type
# of studies
Animal Model

No Animal Model Data Available


Interactor Symbol Interactor Name Interactor Organism Entrez ID Uniprot ID Interaction Type Evidence Reference
DGUOK deoxyguanosine kinase 1716 E5KSL5 IP; LC-MS/MS
Huttlin EL , et al. 2015
NUFIP1 Nuclear FMRP Interacting Protein 1 26747 Q9UHK0 IP; LC-MS/MS
Huttlin EL , et al. 2015
Grik2 glutamate receptor, ionotropic, kainate 2 (beta 2) 14806 P39087 IP/WB; Co-localization
Mahadevan V , et al. 2014
Neto2 neuropilin (NRP) and tolloid (TLL)-like 2 74513 Q8BNJ6 IP; LC-MS/MS; IP/WB
Ivakine EA , et al. 2013
Neto2 neuropilin (NRP) and tolloid (TLL)-like 2 74513 Q8BNJ6 IP/WB; Co-localization
Mahadevan V , et al. 2014
Arhgef7 Rho guanine nucleotide exchange factor (GEF7) 114559 O55043 Y2H; IP/WB; Co-localization
Llano O , et al. 2015
Epb41l1 erythrocyte membrane protein band 4.1-like 1 59317 Q9WTP0 IP/WB
Li H , et al. 2007

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