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Relevance to Autism

Two de novo variants in the SETD1B gene (an inframe deletion variant and a missense variant) were identified in ASD probands from the Simons Simplex Collection in Iossifov et al., 2014. SETD1B has been implicated as a candidate gene in 12q24.31 microdeletion syndrome, a disorder characterized by intellectual disability, autism/autistic features, epilepsy, and facial dysmorphic features (Baple et al., 2010; Qiao et al., 2013; Palumbo et al., 2015; Labonne et al., 2016). Hiraide et al., 2018 identified two individuals with novel de novo SETD1B missense variants, both of whom were diagnosed with autism/ASD and presented with intellectual disability, language delay, and epilepsy.

Molecular Function

SET1B is a component of a histone methyltransferase complex that produces trimethylated histone H3 at Lys4; H3 'Lys-4' methylation represents a specific tag for epigenetic transcriptional activation.

External Links

        

References

Type
Title
Type of Disorder
Associated Disorders
Author, Year
Primary
The contribution of de novo coding mutations to autism spectrum disorder
ASD
Support
Integrating de novo and inherited variants in 42
ASD
Support
Clinical application of 2.7M Cytogenetics array for CNV detection in subjects with idiopathic autism and/or intellectual disability.
12q24.31 microdeletion syndrome
Support
A genome-wide DNA methylation signature for SETD1B-related syndrome
Intellectual developmental disorder with seizures
Support
Trio-based exome sequencing reveals a high rate of the de novo variants in intellectual disability
ID, epilepsy/seizures
Support
A microdeletion at 12q24.31 can mimic beckwith-wiedemann syndrome neonatally.
12q24.31 microdeletion syndrome
Support
De novo variants in SETD1B cause intellectual disability, autism spectrum disorder, and epilepsy with myoclonic absences.
ASD, ID, epilepsy/seizures
Support
Diagnostic yield of next-generation sequencing in 87 families with neurodevelopmental disorders
DD, ID, epilepsy/seizures
Support
Inherited and De Novo Genetic Risk for Autism Impacts Shared Networks.
ASD
Support
Postnatal expression of the lysine methyltransferase SETD1B is essential for learning and the regulation of neuron-enriched genes
Support
A novel de novo frameshift variant in SETD1B causes epilepsy.
DD, ID, epilepsy/seizures
Autistic features
Support
Genetic and phenotypic analysis of 101 patients with developmental delay or intellectual disability using whole-exome sequencing
ASD, DD, epilepsy/seizures
Support
ASD
ADHD, BPD, OCD, ID, learning disability
Support
An atypical 12q24.31 microdeletion implicates six genes including a histone demethylase KDM2B and a histone methyltransferase SETD1B in syndromic i...
12q24.31 microdeletion syndrome
Support
De novo variants in neurodevelopmental disorders-experiences from a tertiary care center
ASD, DD, epilepsy/seizures
Support
DD, epilepsy/seizures
Autistic features
Support
Microdeletion of 12q24.31: report of a girl with intellectual disability, stereotypies, seizures and facial dysmorphisms.
12q24.31 microdeletion syndrome
Support
SETD1B-associated neurodevelopmental disorder
DD, ID, epilepsy/seizures
ASD, ADHD
Recent Recommendation
Delineating the molecular and phenotypic spectrum of the SETD1B-related syndrome
DD, ID, epilepsy/seizures
ASD or autistic features
Recent Recommendation
De novo variants in SETD1B are associated with intellectual disability, epilepsy and autism.
ASD, ID, epilepsy/seizures

Rare

Variant ID
Variant Type
Allele Change
Residue Change
Inheritance Pattern
Inheritance Association
Family Type
Author, Year
 GEN994R001 
 inframe_deletion 
 c.5690_5695del 
 p.Thr1897_Asp1899delinsAsn 
 De novo 
  
 Simplex 
 GEN994R002 
 missense_variant 
 c.3884C>T 
 p.Pro1295Leu 
 De novo 
  
 Simplex 
 GEN994R003 
 missense_variant 
 c.5524C>T 
 p.Arg1842Trp 
 De novo 
  
  
 GEN994R004 
 missense_variant 
 c.5575C>T 
 p.Gln1859Ter 
 De novo 
  
  
 GEN994R005 
 frameshift_variant 
 c.5645_5648del 
 p.Tyr1882CysfsTer34 
 De novo 
  
 Simplex 
 GEN994R006 
 missense_variant 
 c.1658G>A 
 p.Gly553Asp 
 De novo 
  
 Multiplex 
 GEN994R007 
 missense_variant 
 c.386T>G 
 p.Val129Gly 
 De novo 
  
 Simplex 
 GEN994R008 
 splice_site_variant 
 c.5589+1G>A 
  
 De novo 
  
 Simplex 
 GEN994R009 
 stop_gained 
 c.3964C>T 
 p.Gln1322Ter 
 De novo 
  
 Simplex 
 GEN994R010 
 missense_variant 
  
  
 De novo 
  
 Simplex 
 GEN994R011 
 stop_gained 
 c.2932C>T 
 p.Gln978Ter 
 De novo 
  
  
 GEN994R012 
 missense_variant 
 c.5699A>G 
 p.Tyr1900Cys 
 De novo 
  
 Unknown 
 GEN994R013 
 missense_variant 
 c.5704C>T 
 p.Arg1902Cys 
 De novo 
  
 Simplex 
 GEN994R014 
 frameshift_variant 
 c.22dup 
 p.His8ProfsTer30 
 De novo 
  
 Simplex 
 GEN994R015 
 frameshift_variant 
 c.22dup 
 p.His8ProfsTer30 
 De novo 
  
 Simplex 
 GEN994R016a 
 missense_variant 
 c.30C>A 
 p.His10Gln 
 Familial 
  
 Simplex 
 GEN994R016b 
 missense_variant 
 c.2780G>A 
 p.Arg927His 
 Familial 
  
 Simplex 
 GEN994R017a 
 missense_variant 
 c.282G>C 
 p.Glu94Asp 
 Familial 
  
  
 GEN994R017b 
 missense_variant 
 c.3982C>T 
 p.Pro1328Ser 
 Familial 
  
  
 GEN994R018 
 frameshift_variant 
 c.284_286delinsA 
 p.Phe95Ter 
 De novo 
  
 Simplex 
 GEN994R019 
 frameshift_variant 
 c.288del 
 p.Tyr96Ter 
 De novo 
  
 Simplex 
 GEN994R020 
 inversion 
 c.337_363inv 
 p.Asn113_Asp121delinsValProGlnGluValPheThrAspVal 
 De novo 
  
 Simplex 
 GEN994R021 
 missense_variant 
 c.509T>C 
 p.Met170Thr 
 De novo 
  
 Simplex 
 GEN994R022 
 missense_variant 
 c.584G>T 
 p.Gly195Val 
 De novo 
  
 Simplex 
 GEN994R023 
 missense_variant 
 c.842C>T 
 p.Thr281Ile 
 Familial 
 Paternal 
  
 GEN994R024a 
 missense_variant 
 c.953C>T 
 p.Thr318Met 
 Familial 
 Both parents 
 Multiplex 
 GEN994R025 
 frameshift_variant 
 c.1234del 
 p.Glu412LysfsTer96 
 Familial 
 Maternal 
  
 GEN994R026 
 missense_variant 
 c.1285C>T 
 p.Arg429Trp 
 De novo 
  
 Simplex 
 GEN994R027 
 missense_variant 
 c.1634C>G 
 p.Pro545Arg 
 Unknown 
  
  
 GEN994R028 
 missense_variant 
 c.2092C>T 
 p.Pro698Ser 
 De novo 
  
 Simplex 
 GEN994R029 
 missense_variant 
 c.2378C>G 
 p.Pro793Arg 
 De novo 
  
 Simplex 
 GEN994R030 
 missense_variant 
 c.2945G>A 
 p.Arg982Gln 
 Unknown 
  
  
 GEN994R031 
 missense_variant 
 c.3029C>T 
 p.Ala1010Val 
 De novo 
  
 Simplex 
 GEN994R032 
 missense_variant 
 c.3386C>T 
 p.Ala1129Val 
 De novo 
  
 Simplex 
 GEN994R033 
 stop_gained 
 c.3985C>T 
 p.Arg1329Ter 
 De novo 
  
 Simplex 
 GEN994R034 
 missense_variant 
 c.4271G>A 
 p.Arg1424Gln 
 De novo 
  
 Simplex 
 GEN994R035 
 stop_gained 
 c.4570C>T 
 p.Arg1524Ter 
 De novo 
  
 Simplex 
 GEN994R036 
 stop_gained 
 c.4996C>T 
 p.Gln1666Ter 
 De novo 
  
 Simplex 
 GEN994R037 
 frameshift_variant 
 c.5184_5185del 
 p.Ala1730Ter 
 De novo 
  
 Simplex 
 GEN994R038 
 missense_variant 
 c.5242C>T 
 p.Arg1748Cys 
 De novo 
  
 Simplex 
 GEN994R039 
 missense_variant 
 c.5374C>T 
 p.Arg1792Trp 
 De novo 
  
 Simplex 
 GEN994R040 
 missense_variant 
 c.5474G>C 
 p.Arg1825Pro 
 De novo 
  
 Simplex 
 GEN994R041 
 missense_variant 
 c.5480A>G 
 p.Lys1827Arg 
 De novo 
  
 Simplex 
 GEN994R042 
 missense_variant 
 c.5702C>T 
 p.Ala1901Val 
 De novo 
  
 Simplex 
 GEN994R043 
 missense_variant 
 c.5702C>A 
 p.Ala1901Glu 
 De novo 
  
 Simplex 
 GEN994R044 
 frameshift_variant 
 c.5820_5826del 
 p.Tyr1941IlefsTer101 
 De novo 
  
 Simplex 
 GEN994R045 
 missense_variant 
 c.5842G>A 
 p.Glu1948Lys 
 De novo 
  
 Simplex 
 GEN994R046 
 missense_variant 
 c.5842G>A 
 p.Glu1948Lys 
 De novo 
  
 Simplex 
 GEN994R047 
 missense_variant 
 c.5842G>A 
 p.Glu1948Lys 
 De novo 
  
 Simplex 
 GEN994R048 
 missense_variant 
 c.5842G>A 
 p.Glu1948Lys 
 De novo 
  
 Simplex 
 GEN994R049 
 stop_gained 
 c.3772C>T 
 p.Arg1258Ter 
 De novo 
  
 Simplex 
 GEN994R050 
 frameshift_variant 
 c.3026_3048del 
 p.Leu1009ArgfsTer88 
 De novo 
  
  
 GEN994R051 
 frameshift_variant 
 c.22del 
 p.His8ThrfsTer27 
 De novo 
  
  
 GEN994R052 
 synonymous_variant 
 c.1071C>T 
 p.Val357%3D 
 De novo 
  
 Multiplex 
 GEN994R053 
 synonymous_variant 
 c.3807T>C 
 p.Pro1269%3D 
 De novo 
  
 Simplex 
 GEN994R054 
 missense_variant 
 c.4577C>T 
 p.Pro1526Leu 
 De novo 
  
 Multiplex 
 GEN994R055 
 missense_variant 
 c.5407C>T 
 p.Arg1803Cys 
 De novo 
  
 Simplex 
 GEN994R056 
 synonymous_variant 
 c.5415G>A 
 p.Leu1805%3D 
 De novo 
  
 Simplex 
 GEN994R057 
 missense_variant 
 c.5704C>T 
 p.Arg1902Cys 
 Unknown 
  
 Simplex 
 GEN994R058 
 missense_variant 
 c.30C>A 
 p.His10Gln 
 Familial 
 Maternal 
 Multiplex 
  et al.  

Common

No Common Variants Available
Chromosome
CNV Locus
CNV Type
# of studies
Animal Model
12
Duplication
 1
 
12
Duplication
 3
 
12
Duplication
 1
 
12
Duplication
 1
 
12
Deletion-Duplication
 26
 
12
Deletion-Duplication
 2
 

No Animal Model Data Available

 

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