HELP     Sign In
Search

Relevance to Autism

De novo missense variants in the SETD1A gene were identified in two ASD probands (Yuen et al., 2017), while a de novo likely gene-disruptive variant in this gene was observed in an ASD proband from the SPARK cohort (Feliciano et al., 2019). Kummeling et al., 2020 reported 15 individuals with de novo SETD1A variants presenting with a novel neurodevelopmental syndrome characterized by global developmental delay and/or intellectual disability, behavioral/psychiatric abnormalities, and craniofacial dysmorphisms; 3/14 individuals in this cohort presented with autistic behavior.

Molecular Function

The protein encoded by this gene is a component of a histone methyltransferase (HMT) complex that produces mono-, di-, and trimethylated histone H3 at Lys4. Trimethylation of histone H3 at lysine 4 (H3K4me3) is a chromatin modification known to generally mark the transcription start sites of active genes. The protein contains SET domains, a RNA recognition motif domain and is a member of the class V-like SAM-binding methyltransferase superfamily.

External Links

        

References

Type
Title
Type of Disorder
Associated Disorders
Author, Year
Primary
Whole genome sequencing resource identifies 18 new candidate genes for autism spectrum disorder
ASD
Positive Association
Irritability
Support
Mutational Landscape of Autism Spectrum Disorder Brain Tissue
ASD
Support
Exome sequencing of 457 autism families recruited online provides evidence for autism risk genes
ASD
Support
DD, epilepsy/seizures
Support
DD, ID
Autistic features
Support
Integrating de novo and inherited variants in 42
ASD
Support
Genetic investigation of syndromic forms of obesity
DD, ID
Autistic features
Support
Loss-of-function variants in the schizophrenia risk gene SETD1A alter neuronal network activity in human neurons through the cAMP/PKA pathway
Schizophrenia
Recent Recommendation
Characterization of SETD1A haploinsufficiency in humans and Drosophila defines a novel neurodevelopmental syndrome
DD, ID
Recent Recommendation
Rare coding variants in ten genes confer substantial risk for schizophrenia
Schizophrenia

Rare

Variant ID
Variant Type
Allele Change
Residue Change
Inheritance Pattern
Inheritance Association
Family Type
Author, Year
 GEN1176R001 
 missense_variant 
 c.2740C>T 
 p.Pro914Ser 
 De novo 
  
 Simplex 
 GEN1176R002 
 missense_variant 
 c.4246G>A 
 p.Glu1416Lys 
 De novo 
  
 Multiplex 
 GEN1176R003 
 frameshift_variant 
 c.1381dup 
 p.Arg461ProfsTer18 
 De novo 
  
  
 GEN1176R004 
 stop_gained 
 c.109C>T 
 p.Gln37Ter 
 De novo 
  
  
 GEN1176R005 
 frameshift_variant 
 c.1014dup 
 p.Ala339ArgfsTer23 
 De novo 
  
  
 GEN1176R006 
 frameshift_variant 
 c.1144_1147del 
 p.Tyr382HisfsTer114 
 De novo 
  
  
 GEN1176R007 
 stop_gained 
 c.1363G>T 
 p.Glu455Ter 
 De novo 
  
  
 GEN1176R008 
 stop_gained 
 c.1495C>T 
 p.Gln499Ter 
 De novo 
  
  
 GEN1176R009 
 frameshift_variant 
 c.1602_1603del 
 p.Gly535AlafsTer12 
 De novo 
  
  
 GEN1176R010 
 frameshift_variant 
 c.2289dup 
 p.Val764SerfsTer61 
 De novo 
  
  
 GEN1176R011 
 stop_gained 
 c.2725G>T 
 p.Glu909Ter 
 De novo 
  
  
 GEN1176R012 
 stop_gained 
 c.2968C>T 
 p.Arg990Ter 
 De novo 
  
  
 GEN1176R013 
 frameshift_variant 
 c.3937_3947del 
 p.Pro1313AlafsTer17 
 Unknown 
 Not maternal 
  
 GEN1176R014 
 frameshift_variant 
 c.3982_3983del 
 p.Phe1328GlnfsTer5 
 De novo 
  
  
 GEN1176R015 
 splice_site_variant 
 c.4409-2A>G 
  
 De novo 
  
  
 GEN1176R016 
 missense_variant 
 c.4495T>G 
 p.Tyr1499Asp 
 De novo 
  
  
 GEN1176R017 
 splice_site_variant 
 c.4582-2_4582del 
  
 De novo 
  
  
 GEN1176R018 
 splice_site_variant 
 c.4582-2_4582del 
  
 De novo 
  
  
 GEN1176R019 
 synonymous_variant 
 c.252C>T 
 p.Asp84%3D 
 Unknown 
  
  
 GEN1176R020 
 missense_variant 
 c.2761G>A 
 p.Asp921Asn 
 Familial 
 Paternal 
 Extended multiplex 
 GEN1176R021 
 missense_variant 
 c.821C>T 
 p.Thr274Met 
 De novo 
  
  
 GEN1176R022 
 missense_variant 
 c.3935C>T 
 p.Ala1312Val 
 De novo 
  
  
 GEN1176R023 
 missense_variant 
 c.2481G>C 
 p.Trp827Cys 
 De novo 
  
  
 GEN1176R024 
 missense_variant 
 c.2690G>A 
 p.Arg897Gln 
 De novo 
  
  
 GEN1176R025 
 missense_variant 
 c.2968C>G 
 p.Arg990Gly 
 De novo 
  
  
 GEN1176R026 
 missense_variant 
 c.3316A>T 
 p.Thr1106Ser 
 De novo 
  
  
 GEN1176R027 
 splice_site_variant 
 c.4582-2_4582-1del 
  
 De novo 
  
  
 GEN1176R028 
 synonymous_variant 
 c.3012G>A 
 p.Ser1004%3D 
 De novo 
  
 Simplex 
 GEN1176R029 
 stop_gained 
 c.7C>T 
 p.Gln3Ter 
 Unknown 
 Not paternal 
  
 GEN1176R030 
 frameshift_variant 
 c.3005_3006del 
 p.Glu1002GlyfsTer20 
 De novo 
  
 Simplex 
  et al.  

Common

Variant ID
Polymorphism
SNP ID
Allele Change
Residue Change
Population Origin
Population Stage
Author, Year
 GEN1176C001 
 intron_variant 
 rs2054213 
 c.247-778A>T 
  
 105,975 cases with self-reported irritability and 273,531 controls (all of European ancestry) from the UK Biobank 
 Discovery 
Chromosome
CNV Locus
CNV Type
# of studies
Animal Model
16
Deletion-Duplication
 139
  construct
16
Deletion
 1
 
16
Deletion
 1
 

No Animal Model Data Available

 

No Interactions Available
HELP
Copyright © 2017 MindSpec, Inc.