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Relevance to Autism

A de novo frameshift variant and several de novo missense variants in the LHX2 gene have been identified in ASD probands from the Autism Sequencing Consortium and the SPARK cohort (Satterstrom et al., 2020; Zhou et al., 2022; Trost et al., 2022). Schmid et al., 2023 reported 19 individuals from 18 families, including the three ASD probands from the SPARK cohort, with LHX2 variation and presenting with a variable neurodevelopmental disorder characterized by developmental delay, autism spectrum disorder and other behavioral abnormalities, variable intellectual disability, and microcephaly; four of the LHX2 missense variants identified in affected individuals, including one that was observed in a SPARK ASD proband, were shown experimentally to result in nucleolar accumulation, impaired interaction with co-factor LDB1, and/or reduced transcriptional activation by luciferase assay.

Molecular Function

This gene encodes a protein belonging to a large protein family, members of which carry the LIM domain, a unique cysteine-rich zinc-binding domain. The encoded protein may function as a transcriptional regulator. The protein can recapitulate or rescue phenotypes in Drosophila caused by a related protein, suggesting conservation of function during evolution.

External Links

        

References

Type
Title
Type of Disorder
Associated Disorders
Author, Year
Primary
DD
ASD or autistic features, ADHD, ID
Support
Large-Scale Exome Sequencing Study Implicates Both Developmental and Functional Changes in the Neurobiology of Autism
ASD
Support
Genomic architecture of autism from comprehensive whole-genome sequence annotation
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
 GEN1399R001 
 missense_variant 
 c.809G>T 
 p.Arg270Leu 
 De novo 
  
  
 GEN1399R002 
 missense_variant 
 c.238T>A 
 p.Cys80Ser 
 De novo 
  
 Simplex 
 GEN1399R003 
 missense_variant 
 c.644A>G 
 p.Asn215Ser 
 De novo 
  
 Simplex 
 GEN1399R004 
 frameshift_variant 
 c.187del 
 p.Arg63AlafsTer66 
 De novo 
  
 Simplex 
 GEN1399R005 
 copy_number_loss 
  
  
 Unknown 
 Not maternal 
 Unknown 
 GEN1399R006 
 frameshift_variant 
 c.272dup 
 p.Thr92HisfsTer8 
 De novo 
  
 Simplex 
 GEN1399R007 
 frameshift_variant 
 c.289_293del 
 p.Asp97Ter 
 Unknown 
  
 Simplex 
 GEN1399R008 
 frameshift_variant 
 c.338_351del 
 p.Gln113LeufsTer30 
 Unknown 
  
 Unknown 
 GEN1399R009 
 stop_gained 
 c.589A>T 
 p.Lys197Ter 
 De novo 
  
 Simplex 
 GEN1399R010 
 stop_gained 
 c.639C>A 
 p.Tyr213Ter 
 De novo 
  
 Simplex 
 GEN1399R011 
 frameshift_variant 
 c.706del 
 p.Asp236IlefsTer9 
 Unknown 
  
 Simplex 
 GEN1399R012 
 stop_gained 
 c.938G>A 
 p.Trp313Ter 
 De novo 
  
 Simplex 
 GEN1399R013 
 frameshift_variant 
 c.978_981del 
 p.Leu326PhefsTer41 
 De novo 
  
 Simplex 
 GEN1399R014 
 frameshift_variant 
 c.982_994dup 
 p.Gly332AlafsTer45 
 De novo 
  
 Simplex 
 GEN1399R015 
 missense_variant 
 c.437G>A 
 p.Cys146Tyr 
 De novo 
  
 Simplex 
 GEN1399R016 
 missense_variant 
 c.948C>G 
 p.Asn316Lys 
 De novo 
  
 Simplex 
 GEN1399R017 
 missense_variant 
 c.953G>T 
 p.Arg318Leu 
 Familial 
 Maternal 
  
 GEN1399R018 
 missense_variant 
 c.880A>G 
 p.Lys294Glu 
 De novo 
  
  
 GEN1399R019 
 missense_variant 
 c.621C>A 
 p.Asn207Lys 
 De novo 
  
  

Common

No Common Variants Available
Chromosome
CNV Locus
CNV Type
# of studies
Animal Model
9
Duplication
 1
 
9
Deletion
 1
 
9
Duplication
 1
 
9
Deletion-Duplication
 6
 

No Animal Model Data Available

 

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