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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
ASD
DD, ID
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
High prevalence of multilocus pathogenic variation in neurodevelopmental disorders in the Turkish population
DD, ID
Support
Genes that Affect Brain Structure and Function Identified by Rare Variant Analyses of Mendelian Neurologic Disease.
ID
Microcephaly
Support
ID
ASD, epilepsy/seizures
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
X-linked alpha-thalassemia/impaired intellectual d
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
X-linked intellectual disability-hypotonic facies
Support
Targeted sequencing and functional analysis reveal brain-size-related genes and their networks in autism spectrum disorders.
ASD
Support
Splicing mutation in the ATR-X gene can lead to a dysmorphic mental retardation phenotype without alpha-thalassemia.
ID
Autistic behavior
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
Brief Report: Evidence of Autism Spectrum Disorder Caused by a Mutation in ATRX Gene: A Case Report
ASD, DD, ID
Support
Using medical exome sequencing to identify the causes of neurodevelopmental disorders: experience of two clinical units and 216 patients.
ID
Support
Mutations in a putative global transcriptional regulator cause X-linked mental retardation with alpha-thalassemia (ATR-X syndrome).
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
Genetic care in geographically isolated small island communities: 8 years of experience in the Dutch Caribbean
ID
Support
Genomic diagnosis for children with intellectual disability and/or developmental delay.
ID
Hypotonia, spasticity
Support
ASD
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
Prevalence and phenotypic impact of rare potentially damaging variants in autism spectrum disorder
ASD
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 
  
 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 
  
  
 GEN288R038 
 missense_variant 
 c.2388A>C 
 p.Lys796Asn 
 Familial 
 Maternal 
 Simplex 
 GEN288R039 
 missense_variant 
 c.533T>C 
 p.Val178Ala 
 Unknown 
  
  
 GEN288R040 
 frameshift_variant 
 c.7367_7371del 
 p.Met2456ArgfsTer40 
 De novo 
  
  
 GEN288R041 
 missense_variant 
 c.4862C>T 
 p.Thr1621Met 
 Familial 
 Maternal 
 Simplex 
 GEN288R042 
 copy_number_loss 
  
  
 Familial 
 Maternal 
 Simplex 
 GEN288R043a 
 missense_variant 
 c.1085C>T 
 p.Thr362Ile 
 Familial 
 Both parents 
 Simplex 
 GEN288R044 
 splice_region_variant 
 c.4957-4A>G 
  
 Familial 
 Maternal 
 Multiplex 
 GEN288R045 
 missense_variant 
 c.4921T>C 
 p.Trp1641Arg 
 Unknown 
  
 Simplex 

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
 21
 
X
Deletion
 2
 
X
Duplication
 1
 
X
Duplication
 1
 
X
Duplication
 1
 
X
Deletion-Duplication
 16
 
X
Deletion
 1
 

Model Summary

The Atrx mutant mouse model shows alterations in behavior, with mutants exhibiting decreased conditioned fear response and spatial learning. Additionally, mice display increased aggression, as measured by an increased number of tail rattling events in the three-chamber social approach test, increased agitation in the presence of a handler as quantified by a score that reflects biting, trunk curl and vocalization, and decreased latency to attack in male mice in the resident-intruder test. Male mutants also exhibit increased depression as measured by an increase in the time spent immobile in the forced swim test. The model also shows sensory deficits, as demonstrated by diminished olfaction.

References

Type
Title
Author, Year
Primary

M_ATRX_1_CKO_HM

Model Type: Genetic
Model Genotype: Homozygous
Mutation: Mice were generated with conditional inactivation of Atrx in post- mitotic excitatory neurons starting at E11.5, by crossing 129SV female mice heterozygous for Atrx^loxP sites (MGI:3528480) with C57BL/6 male mice expressing Cre recombinase under the control of NEX-Cre gene promotor (MGI:2668659). To obtain homozygous Atrx^loxP females, 129SV female mice heterozygous for Atrx^loxP sites were crossed with C57BL/6;129SV male mice expressing NEX-Cre and have a floxed Atrx allele, offspring homozygous for Atrx^loxP expressing NEX-Cre were knockouts.
Allele Type: Conditional knockout
Strain of Origin: 129P2/OlaHsd; (129X1/SvJ x 129S1/Sv)F1-Kitl+
Genetic Background: 129SV x C57BL/6;129SV
ES Cell Line: E14TG2a; R1
Mutant ES Cell Line:
Model Source: Richard Gibbons; Klaus-Armin Nave

M_ATRX_1_CKO_HM

Category
Entity
Quantity
Experimental Paradigm
Age at Testing
General locomotor activity1
Increased
Description: ATRX mutant mice exhibited a significant increase in total distance travelled, average velocity, and total distance travelled in the center compared to controls.
 Open field test
 3-6 months
Swimming ability1
Decreased
Description: ATRX mutant mice exhibited a significant decrease in the percentage of time spent swimming compared to controls.
 Morris water maze test
 3-6 months
Self scratching1
Increased
Description: ATRX mutant mice exhibited increased instances of self scratching compared to controls.
 Grooming behavior assessments
 3-6 months
Self grooming1
Increased
Description: ATRX mutant mice exhibited a significantly increased amount of time spent grooming compared to controls.
 Grooming behavior assessments
 3-6 months
Startle response: acoustic stimulus1
Increased
Description: ATRX mutant male mice exhibited a significantly increased startle response to an acoustic stimulus compared to controls.
 Prepulse inhibition
 3-6 months
Sensorimotor gating1
Decreased
Description: ATRX mutant male mice displayed significantly decreased pre-pulse inhibition compared to controls.
 Prepulse inhibition
 3-6 months
Sensorimotor gating1
Decreased
Description: ATRX mutant female mice displayed no change in pre-pulse inhibition compared to controls.
 Prepulse inhibition
 3-6 months
Olfaction1
Decreased
Description: ATRX mutant male and female mice exhibited significantly decreased amounts of time spent sniffing an almond and banana compared to controls.
 Response to olfactory stimuli
 3-6 months
Aggression1
Increased
Description: ATRX mutant male mice exhibited significantly more tail rattling events at a stranger mouse compared to controls.
Exp Paradigm: stranger mouse in chamber 1 (s1), object in chamber 2
 Three-chamber social approach test
 3-6 months
Aggression1
Increased
Description: ATRX mutant male mice exhibited a decreased latency to attack compared to controls, showing a significant increase in aggression.
 Resident-intruder test
 3-6 months
Aggression1
Increased
Description: ATRX mutant male and female mice exhibited increased agitation in the presence of a handler compared to controls, as quantified by a score that reflects biting, trunk curl and vocalization events during handling.
 General observations
 3-6 months
Anxiety1
Increased
Description: ATRX mutant mice exhibited a significant decrease in the amount of time spent in the dark area compared to controls.
 Light-dark exploration test
 3-6 months
Fear response1
Decreased
Description: ATRX mutant mice spent significantly less time freezing compared to control mice at 1.5 and 24 hours after foot shock.
 Fear conditioning test
 3 months
Depression1
Decreased
Description: ATRX mutant male mice exhibited a significant increase in the percentage of time spent immobile compared to controls.
 Forced swim test
 3-6 months
Depression1
Increased
Description: ATRX mutant female mice exhibited a significant decrease in the percentage of time spent immobile compared to controls.
 Forced swim test
 3-6 months
Spatial learning1
Decreased
Description: ATRX mutant mice exhibited significantly impaired spatial learning compared to control mice, as evidenced by an increased latency to locate the platform.
 Morris water maze test
 3-6 months
Targeted expression1
Decreased
Description: Atrx mutant mice exhibited a decrease in the expression of ATRX protein in the cortical plate compared to controls.
 Immunohistochemistry
 E13.5
Targeted expression1
Decreased
Description: Atrx mutant mice exhibited a decrease in the expression of ATRX protein in NeuN-positive neurons compared to controls.
Exp Paradigm: cortex, hippocampus
 Immunohistochemistry
 P20
Anxiety1
 No change
 Open field test
 3-6 months
General locomotor activity1
 No change
 Light-dark exploration test
 3-6 months
Foot shock sensitivity1
 No change
 Fear conditioning test
 3 months
Startle response: acoustic stimulus1
 No change
 Prepulse inhibition
 3-6 months
Aggression1
 No change
 Three-chamber social approach test
 3-6 months
Aggression1
 No change
 Resident-intruder test
 3-6 months
Social approach1
 No change
 Three-chamber social approach test
 3-6 months
Social memory1
 No change
 Three-chamber social approach test
 3-6 months
 Not Reported:


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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