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Relevance to Autism

A rare mutation in the ATRX gene has been identified with ASD (Gong et al., 2008).

Molecular Function

The protein encoded by this gene contains an ATPase/helicase domain, and thus it belongs to the SWI/SNF family of chromatin remodeling proteins. Mutations in this gene are associated with an X-linked mental retardation (XLMR) syndrome most often accompanied by alpha-thalassemia (ATRX) syndrome. These mutations have been shown to cause diverse changes in the pattern of DNA methylation, which may provide a link between chromatin remodeling, DNA methylation, and gene expression in developmental processes. Multiple alternatively spliced transcript variants encoding distinct isoforms have been reported.

External Links

        

References

Type
Title
Type of Disorder
Associated Disorders
Author, Year
Primary
Alpha thalassaemia-mental retardation, X linked.
ID
Epilepsy, ASD
Support
Novel ATRX gene damaging missense mutation c.6740A>C segregates with profound to severe intellectual deficiency without alpha thalassaemia.
ID
Stereotypies, absent speech
Support
Characterization of intellectual disability and autism comorbidity through gene panel sequencing.
ID, ASD or autistic traits
Support
Hybridisation-based resequencing of 17 X-linked intellectual disability genes in 135 patients reveals novel mutations in ATRX, SLC6A8 and PQBP1.
ID
Support
Mutations in a putative global transcriptional regulator cause X-linked mental retardation with alpha-thalassemia (ATR-X syndrome).
ID
Support
Genes that Affect Brain Structure and Function Identified by Rare Variant Analyses of Mendelian Neurologic Disease.
ID
Microcephaly
Support
Lessons Learned from Large-Scale, First-Tier Clinical Exome Sequencing in a Highly Consanguineous Population.
Macrocephaly, developmental regression
Stereotypies
Support
Analysis of X chromosome inactivation in autism spectrum disorders.
ASD
Support
The landscape of somatic mutation in cerebral cortex of autistic and neurotypical individuals revealed by ultra-deep whole-genome sequencing
ASD
Support
ATRX mutation in two adult brothers with non-specific moderate intellectual disability identified by exome sequencing.
ID, epilepsy/seizures
Support
Exome Pool-Seq in neurodevelopmental disorders.
DD
Hypotonia
Support
Excess of de novo variants in genes involved in chromatin remodelling in patients with marfanoid habitus and intellectual disability
ID
Marfanoid habitus
Support
Large-scale discovery of novel genetic causes of developmental disorders.
ASD, DD
Support
Targeted sequencing and functional analysis reveal brain-size-related genes and their networks in autism spectrum disorders.
ASD
Support
Genetic landscape of autism spectrum disorder in Vietnamese children
ASD
Support
Efficient strategy for the molecular diagnosis of intellectual disability using targeted high-throughput sequencing.
ID
Support
Using medical exome sequencing to identify the causes of neurodevelopmental disorders: experience of two clinical units and 216 patients.
ID
Support
Exome sequencing of 457 autism families recruited online provides evidence for autism risk genes
ASD
Support
Massively parallel sequencing of patients with intellectual disability, congenital anomalies and/or autism spectrum disorders with a targeted gene ...
DD, ID, ASD
MCA
Support
Genomic diagnosis for children with intellectual disability and/or developmental delay.
ID
Hypotonia, spasticity
Support
Impact of on-site clinical genetics consultations on diagnostic rate in children and young adults with autism spectrum disorder.
ASD
Support
Using whole-exome sequencing to identify inherited causes of autism.
ASD
Support
Splicing mutation in the ATR-X gene can lead to a dysmorphic mental retardation phenotype without alpha-thalassemia.
ID
Autistic behavior
Recent Recommendation
Rosiglitazone REMS restrictions removed.

Rare

Variant ID
Variant Type
Allele Change
Residue Change
Inheritance Pattern
Inheritance Association
Family Type
Author, Year
 GEN288R001 
 missense_variant 
 c.5027G>C 
 p.Gly1676Ala 
 Familial 
 Maternal 
 Multiplex 
 GEN288R002 
 missense_variant 
 c.4031A>G 
 p.Lys1344Arg 
 Familial 
 Maternal 
 Simplex 
 GEN288R003 
 copy_number_loss 
  
  
  
  
  
 GEN288R004 
 missense_variant 
 c.2302A>G 
 p.Lys768Glu 
  
  
  
 GEN288R005 
 missense_variant 
 c.2316T>C 
 p.Cys755Arg 
  
  
  
 GEN288R006 
 missense_variant 
 c.2429C>A 
 p.Thr810Asn 
  
  
 Multiplex 
 GEN288R007 
 missense_variant 
 c.3058A>G 
 p.Asn1002Ser 
  
  
  
 GEN288R008 
 missense_variant 
 c.3583A>T 
 p.Arg1195Trp 
  
  
  
 GEN288R009 
 missense_variant 
 c.3729A>G 
 p.Gln1243= 
  
  
  
 GEN288R010 
 missense_variant 
 c.3967A>G 
 p.Tyr1305Cys 
  
  
  
 GEN288R011 
 stop_gained 
 c.4635C>T 
 p.Thr1545= 
  
  
  
 GEN288R012 
 stop_gained 
 c.4641G>T 
 p.Glu1530Ter 
  
  
  
 GEN288R013 
 splice_site_variant 
 T>A 
  
 Familial 
 Maternal 
 Multi-generational 
 GEN288R014 
 missense_variant 
 c.5282T>C 
 p.Met1761Thr 
  
  
  
 GEN288R015 
 stop_gained 
 c.7156C>T 
 p.Arg2386Ter 
 Familial 
 Maternal 
 Multiplex 
 GEN288R016 
 missense_variant 
 c.1825C>G 
 p.Pro609Ala 
 Familial 
 Maternal 
 Multiplex 
 GEN288R017 
 missense_variant 
 c.1565C>G 
 p.Ser522Cys 
 Familial 
 Maternal 
 Multiplex 
 GEN288R018 
 frameshift_variant 
 c.7378dup 
 p.Tyr2460LeufsTer38 
 De novo 
 NA 
 Simplex 
 GEN288R019 
 missense_variant 
 c.6139C>T 
 p.Leu2047= 
 Familial 
 Maternal 
 Multi-generational 
 GEN288R020 
 stop_gained 
 c.109C>T 
 p.Arg37Ter 
 Familial 
 Maternal 
 Multiplex 
 GEN288R021 
 stop_gained 
 c.109C>T 
 p.Arg37Ter 
 Familial 
 Maternal 
 Simplex 
 GEN288R022 
 missense_variant 
 c.1013C>G 
 p.Ser338Cys 
 Familial 
 Maternal 
 Multiplex 
 GEN288R023 
 missense_variant 
 c.308T>A 
 p.Val103Glu 
 Familial 
 Maternal 
 Multiplex 
 GEN288R024 
 missense_variant 
 c.1676C>T 
 p.Ser559Leu 
 Familial 
 Maternal 
 Simplex 
 GEN288R025 
 missense_variant 
 c.6740A>C 
 p.His2247Pro 
 Familial 
 Maternal 
 Multi-generational 
 GEN288R026 
 missense_variant 
 c.1423C>T 
 p.His475Tyr 
 Familial 
 Maternal 
  
 GEN288R027 
 missense_variant 
 c.4865C>T 
 p.Ala1622Val 
 Familial 
 Maternal 
 Multiplex 
 GEN288R028 
 missense_variant 
 c.6280G>A 
 p.Val2094Ile 
 Familial 
  
 Simplex 
 GEN288R029 
 missense_variant 
 c.6863G>A 
 p.Arg2288His 
 Familial 
 Maternal 
  
 GEN288R030 
 missense_variant 
 c.4244A>G 
 p.Asn1415Ser 
 Familial 
 Maternal 
  
 GEN288R031 
 missense_variant 
 c.7253A>T 
 p.Tyr2418Phe 
 Unknown 
  
  
 GEN288R032 
 missense_variant 
 c.6740A>C 
 p.His2247Pro 
 Familial 
 Maternal 
  
 GEN288R033 
 missense_variant 
 c.622C>T 
 p.Arg208Cys 
  
  
 Unknown 
 GEN288R034 
 stop_gained 
 c.109C>T 
 p.Arg37Ter 
 Familial 
 Maternal 
  
 GEN288R035 
 missense_variant 
 c.1972C>T 
 p.Arg658Cys 
 Familial 
 Maternal 
 Simplex 
 GEN288R036 
 stop_gained 
 c.-117C>T 
  
 Familial 
 Maternal 
 Simplex 
 GEN288R037 
 missense_variant 
 ENSG00000085224:ENST00000395603:exon20:c.T5212C:p.F1738L,ENSG00000085224:ENST00000373344:exon21:c.T5 
  
 De novo 
 NA 
  

Common

No Common Variants Available
Chromosome
CNV Locus
CNV Type
# of studies
Animal Model
X
Deletion
 1
 
X
Duplication
 1
 
X
Deletion
 1
 
X
Deletion-Duplication
 18
 
X
Deletion
 2
 
X
Duplication
 1
 
X
Duplication
 1
 
X
Duplication
 1
 
X
Deletion-Duplication
 14
 
X
Deletion
 1
 

No Animal Model Data Available


Interactor Symbol Interactor Name Interactor Organism Entrez ID Uniprot ID Interaction Type Evidence Reference
HIST1H4A histone cluster 1, H4a 8359 B2R4R0 IP; LC-MS/MS
Huttlin EL , et al. 2015
MECP2 methyl CpG binding protein 2 (Rett syndrome) 29386 Q00566 Y2H
Nan X , et al. 2007
MRE11A MRE11 meiotic recombination 11 homolog A (S. cerevisiae) 4361 P49959 IP/WB; Co-localization
Clynes D , et al. 2015
RAD50 RAD50 homolog (S. cerevisiae) 10111 Q92878 IP/WB
Clynes D , et al. 2015
WDR1 WD repeat domain 1 9948 O75083 IP; LC-MS/MS
Huttlin EL , et al. 2015
Daxx Fas death domain-associated protein 13163 O35613 IP/WB
Elssser SJ , et al. 2015
MECP2 methyl CpG binding protein 2 (Rett syndrome) 4204 P51608 qRT-PCR; ChIP; Chromatin conformation capture
Kernohan KD , et al. 2014

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