The aim of this study was the identification of the genetic cause of ASD in the proband of the studied family. We identified the Thr1621Met mutation in the hemizygote state in the exon 18 of ATRX gene by exome sequencing of a targeted gene panel. The variation has been previously registered (rs122445106) in dbSNP data base and has an allelic frequency less than 0,001% according to the Genome Aggregation Database (gnomAD) [26]. Therefore, it is considered a rare mutation. Thr1621Met is located in the helicase domain of the protein, which includes 17-30 exons [5;27] and is considered a ‘hotspot’ where 33% of sequence alterations are clustered [27]. This domain is the enzymatic core of the protein and plays an important role as a chromatin remodeler [8]. The replacement of threonine by methionine implies an important chemical change, from a hydrophilic amino acid to a hydrophobic one. This alteration could disrupt the structural conformation of helicase domain leading to a loss of function of ATRX.
In the multiple sequences alignment (Table 3), we have compared the ATRX human sequence to ATRX homologue proteins from several species such as rabbit, mouse, zebrafish, tropical clawed frog, or pufferfish. The results showed that the mutated residue is highly conserved among all the species, except for the fruit fly, of which the homologue sequence is quite different from the rest, including the human. Threonine residue is specifically part of the highly conserved downstream helicase motif. In fact, Matthew et. al. reported that mutations located in the two following residues to 1621 (Ala1622 and Leu1623) can particularly destabilize the ATRX protein [7].
Table 3
Multiple amino acid sequence alignment of ATRX from different species.
Species
|
Protein (UniProtKB)
|
Alignment
|
H.sapiens
|
P46100
|
T
|
V
|
L
|
L
|
C
|
D
|
K
|
L
|
D
|
F
|
S
|
T
|
A
|
L
|
V
|
V
|
C
|
P
|
L
|
N
|
T
|
A
|
L
|
P.troglodytes
|
K7AL80
|
T
|
V
|
L
|
L
|
C
|
D
|
K
|
L
|
D
|
F
|
S
|
T
|
A
|
L
|
V
|
V
|
C
|
P
|
L
|
N
|
T
|
A
|
L
|
O.cuniculus
|
G1STD0
|
T
|
V
|
L
|
L
|
C
|
D
|
K
|
L
|
D
|
F
|
S
|
T
|
A
|
L
|
V
|
V
|
C
|
P
|
L
|
N
|
T
|
A
|
L
|
M.musculus
|
Q61687
|
T
|
V
|
L
|
L
|
C
|
D
|
K
|
L
|
D
|
F
|
S
|
T
|
A
|
L
|
V
|
V
|
C
|
P
|
L
|
N
|
T
|
A
|
L
|
G.gallus
|
E1C8H5
|
T
|
V
|
L
|
L
|
C
|
D
|
K
|
L
|
N
|
F
|
R
|
T
|
A
|
L
|
V
|
V
|
C
|
P
|
L
|
N
|
T
|
A
|
L
|
T.rubripes
|
H2T6G5
|
T
|
L
|
L
|
L
|
C
|
E
|
K
|
L
|
K
|
F
|
S
|
T
|
A
|
L
|
V
|
-
|
-
|
-
|
-
|
-
|
-
|
-
|
-
|
D.rerio
|
F1QJ36
|
T
|
V
|
L
|
L
|
C
|
E
|
K
|
L
|
N
|
F
|
S
|
T
|
A
|
L
|
V
|
V
|
C
|
P
|
L
|
N
|
T
|
V
|
L
|
D.melanogaster
|
Q9GQN5
|
T
|
L
|
L
|
V
|
T
|
R
|
R
|
T
|
G
|
V
|
D
|
R
|
V
|
L
|
I
|
I
|
S
|
P
|
L
|
-
|
-
|
-
|
-
|
X.tropicalis
|
F7A8S5
|
T
|
V
|
L
|
L
|
S
|
E
|
K
|
L
|
D
|
F
|
S
|
T
|
A
|
L
|
V
|
V
|
C
|
P
|
L
|
N
|
T
|
V
|
L
|
G.aculeatus
|
G3QAH0
|
T
|
V
|
L
|
L
|
S
|
E
|
N
|
L
|
K
|
F
|
R
|
T
|
A
|
L
|
V
|
V
|
C
|
P
|
L
|
N
|
T
|
I
|
L
|
C.griseus
|
G3HNY0
|
T
|
V
|
L
|
L
|
C
|
D
|
K
|
L
|
D
|
F
|
S
|
T
|
A
|
L
|
V
|
V
|
C
|
P
|
L
|
N
|
T
|
A
|
L
|
T.nigroviridis
|
Q4S8S6
|
T
|
V
|
L
|
L
|
S
|
E
|
N
|
L
|
K
|
F
|
R
|
T
|
A
|
L
|
V
|
I
|
C
|
P
|
L
|
N
|
T
|
V
|
L
|
Sequence alignment was generated by Blastp. Threonine residue is highlighted and the amino acids that differ from those of the human sequence are in bold. |
Mutations in ATRX gene are typically associated with ATRX syndrome. This pathology is characterized by its wide range of phenotypic variability including alpha-thalassaemia, intellectual deficiency, speech delayed, learning difficulties or facial dysmorphism. Thr1621Met missense mutation has been previously described in only one family from Germany with ATRX syndrome and phenotypic variability among their members like different levels of intellectual disability and presence of alpha-thalassaemia in 3 out of the 4 members. No key signs of ASD diagnosis were reported [28]. Accordingly, as far as we concerned, this is the first time that an ATRX Thr1621 mutation is associated with a typical “nonsyndromic autism” case.
Comparing the clinical features of our case to those of the reported family (Table 4), only two clinical manifestations were shared, speech delayed and intellectual deficiency. Curiously, both features can frequently appear in ASD as well as ATRX syndrome. Other typical ATRX syndrome features such as facial hypotonia or alpha-talassaemia were exclusively manifested in ATRX syndrome family, but not in all members, suggesting other modifier factors in this family. It can also no longer be ruled out the frequent co-morbid manifestations of ASD and the need to examine other families with the same mutation to elucidate the genotype-phenotype relationship. ATRX syndrome and ASD overlapping symptoms suggest a common molecular mechanism through ATRX mutations by which either of these pathologies could develop depending on other genetic, epigenetic and/or environmental factors.
able 4
Comparison of clinical features between the patient reported here and four family members reported by Yntema et al.
Clinical features
|
López-Garrido et al
|
Yntema et al
|
Microcephaly
|
NO
|
NO
|
Facial dysmorphism
|
NO
|
No obvious
|
Hypotonia
|
NO
|
YES (facial hypotonia in childhood in some members of the family)
|
Seizures
|
NO, but there is epileptogenic activity
|
NO
|
Speech delayed
|
YES
|
YES
|
Intelectual deficiency
|
YES
|
YES (ranging from borderline to moderate)
|
Alpha-thalassemia
|
NO
|
YES (in 3 out of the 4 members)
|
Chaotic behaviour
|
NO
|
YES
|
Agressive outburst
|
NO
|
YES
|
Urogenital malformations
|
NO
|
NO
|
All the cases have Thr1621Met mutation in ATRX gene. It is only shown the clinical features reported by Yntema et al. |
As far as we know, only another ATRX mutation has been previously reported in two siblings diagnosed with ASD [16] highlighting the multifactorial nature of ASD in contrast to ATRX syndrome monogenetic character. The mutation reported by Gong and co-workers (p.Gly1676Ala) is interestingly located near Thr1621Met, just one exon downstream and in the helicase domain of the protein as well. Unfortunately, Gong et al. did not report any clinical features of the probands beyond an ASD diagnosis, and a phenotypic comparative study could not be complete.
Furthermore, a novel ATRX gene missense mutation (p.His2247Pro) have been recently reported and associated with severe intellectual deficiency without alpha thalassaemia in 3 members of a family [12]. Interestingly, the proband also showed a behavioural disorder associated with stereotypical movements, one of the criteria of ASD diagnosis. This novel mutation is also located in the helicase domain. We can hypothesize ATRX mutations in helicase domain might have an increased susceptibility to develop some sign of ASD while mutations in ADD domain are associated to a severe permanent psychomotor impairment and constant urogenital abnormalities [27]. To confirm this hypothesis, further genotype-phenotype relationship studies would be necessary in a large cohort of patients with ATRX mutations. In any case, we cannot rule out the presence of other altered genes responsible for autism manifestations.
Mutations in the helicase domain have been reported to cause different protein alterations such us destabilization and the resulting dosage change, decrease in ATPase activity by uncoupling ATP hydrolysis or deficiency in DNA translocation [7]. As aforementioned, Thr1621Met also could disrupt the structural conformation of protein, jeopardising the interaction with other chromatin proteins like MeCP2. According to Nan and co-workers, a disruption of MeCP2-ATRX interaction could lead to pathological changes in neural function during brain development [29]. Nevertheless, functional analysis of Thr1621Met would be necessary to clarify the molecular mechanism by which this mutation causes ASD.
The study of chromatin structure has taken an important impetus in recent years and has transcended to the point to understand various human diseases including ASD. ASD-risk genes are often involved in molecular pathways that regulate the synaptic transmission, transcription, and chromatin remodeling during early development. Therefore, we could consider autism like a “synaptic and chromatin-remodeling disorder” [30]. Also, idiopathic autism, which genetic basis are still unclear, could be explain by the above-mentioned epigenetic changes. Carrascosa-Romero and De Cabo-De la Vega stablish a classification of epigenetics of autism in the book "Autism – Paradigms, Recent Research and Clinical Application" [31]. According to these authors, ATP-dependent chromatin remodeling complexes are classified within “Mendelian ASD disorders of the epigenetic machinery in other chromatin remodelers and transcription factors”, where ATRX mutations could be included as a new disorder.