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Relevance to Autism

Two de novo protein-truncating variants in the LDB1 gene were identified in ASD probands from the Autism Sequencing Consortium (De Rubeis et al., 2014; Satterstrom et al., 2020), while additional protein-truncating variants were observed in case and control samples from the Danish iPSYCH study (Satterstrom et al., 2020). TADA analysis of de novo variants from the Simons Simplex Collection and the Autism Sequencing Consortium and protein-truncating variants from iPSYCH in Satterstrom et al., 2020 identified LDB1 as a candidate gene with a false discovery rate (FDR) between 0.01 and 0.05 (0.01 < FDR 0.05).

Molecular Function

Binds to the LIM domain of a wide variety of LIM domain-containing transcription factors. May regulate the transcriptional activity of LIM-containing proteins by determining specific partner interactions. Plays a role in the development of interneurons and motor neurons in cooperation with LHX3 and ISL1. Acts synergistically with LHX1/LIM1 in axis formation and activation of gene expression.

External Links

        

References

Type
Title
Type of Disorder
Associated Disorders
Author, Year
Primary
Synaptic, transcriptional and chromatin genes disrupted in autism.
ASD
Support
Deleterious coding variation associated with autism is shared across ancestries.
ASD
Support
Systematic analysis of variants escaping nonsense-mediated decay uncovers candidate Mendelian diseases
DD
Recent Recommendation
De novo variants in LDB1 are linked to distinct neurodevelopmental phenotypes determined by variant location and differing pathomechanisms.
DD, ID
ASD, ADHD
Recent recommendation
Large-Scale Exome Sequencing Study Implicates Both Developmental and Functional Changes in the Neurobiology of Autism
ASD

Rare

Variant ID
Variant Type
Allele Change
Residue Change
Inheritance Pattern
Inheritance Association
Family Type
Author, Year
 GEN1155R001 
 frameshift_variant 
 c.306del 
 p.Met103CysfsTer2 
 De novo 
  
 Simplex 
 GEN1155R002 
 frameshift_variant 
 c.906del 
 p.Gly304AlafsTer4 
 De novo 
  
 Simplex 
 GEN1155R003 
 missense_variant 
 c.361C>T 
 p.Arg121Trp 
 De novo 
  
 Simplex 
 GEN1155R004 
 frameshift_variant 
 c.938del 
 p.Asn313ThrfsTer25 
 De novo 
  
  
 GEN1155R005 
 frameshift_variant 
 c.849_852del 
 p.Pro284LeufsTer23 
 De novo 
  
  
 GEN1155R006 
 frameshift_variant 
 c.798_799del 
 p.Asp268LeufsTer58 
 Familial 
 Maternal 
  
 GEN1155R007 
 synonymous_variant 
 c.66G>A 
 p.Glu22= 
 De novo 
  
 Multiplex 
 GEN1155R008 
 copy_number_loss 
  
  
 De novo 
  
  
 GEN1155R009 
 copy_number_loss 
  
  
 De novo 
  
  
 GEN1155R010 
 stop_gained 
 c.196C>T 
 p.Gln66Ter 
 De novo 
  
 Simplex 
 GEN1155R011a 
 frameshift_variant 
 c.196del 
 p.Gln66LysfsTer39 
 De novo 
  
 Simplex 
 GEN1155R011b 
 frameshift_variant 
 c.199del 
 p.Thr67LeufsTer38 
 De novo 
  
 Simplex 
 GEN1155R012 
 splice_site_variant 
 c.352+1G>A 
 p.? 
 Unknown 
  
  
 GEN1155R013 
 frameshift_variant 
 c.404dup 
 p.Ala136CysfsTer9 
 De novo 
  
 Simplex 
 GEN1155R014 
 stop_gained 
 c.591G>A 
 p.Trp197Ter 
 De novo 
  
 Simplex 
 GEN1155R015 
 stop_gained 
 c.607C>T 
 p.Gln203Ter 
 De novo 
  
 Simplex 
 GEN1155R016 
 missense_variant 
 c.361C>T 
 p.Arg121Trp 
 De novo 
  
 Simplex 
 GEN1155R017 
 missense_variant 
 c.542G>A 
 p.Arg181Gln 
 De novo 
  
 Simplex 
 GEN1155R018 
 missense_variant 
 c.577C>T 
 p.Arg193Trp 
 De novo 
  
 Simplex 
 GEN1155R019 
 missense_variant 
 c.1075A>C 
 p.Thr359Pro 
 De novo 
  
 Simplex 
 GEN1155R020 
 frameshift_variant 
 c.951del 
 p.Ser317ArgfsTer21 
 De novo 
  
 Simplex 
 GEN1155R021 
 stop_gained 
 c.997C>T 
 p.Gln333Ter 
 De novo 
  
  
 GEN1155R022 
 frameshift_variant 
 c.1068delG 
 p.Arg356SerfsTer127 
 De novo 
  
  

Common

No Common Variants Available
Chromosome
CNV Locus
CNV Type
# of studies
Animal Model
10
Duplication
 1
 
10
Duplication
 1
 
10
Duplication
 1
 
10
Duplication
 2
 

No Animal Model Data Available

 

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