A Novel Pathogenic Hemizygous Variant of AP1S2 Gene in a Child with Dandy-Walker Malformation, Developmental Delay, and Autism
Gayatri Nerakh Department of Genetics, Fernandez Foundation, Hyderabad, Telangana, India. Correspondence to: Dr Gayatri NerakhEmail:maildrgayatri@gmail.com
1 Abstract
There is a high degree of genetic and phenotypic heterogeneity for X-linked intellectual disability. Pettigrew
syndrome is a rare X-linked syndromic intellectual disorder that presents with hydrocephalus with or without
Dandy-Walker malformation (DWM), basal ganglia calcification, developmental delay, autism, and seizures. This is
a report of a male child who presented at the age of 7.5 years with global developmental delay, autism,
and behavioral disturbances. Ultrasound during the antenatal period in the third trimester had revealed
hydrocephalus. Magnetic resonance imaging (MRI) of the brain after birth showed features of hydrocephalus and
DWM. The chromosomal microarray was normal. Trio whole-exome sequencing (WES) revealed a novel
hemizygous pathogenic variant c.286dup (p.Ser96LysfsTer4) [NM_001369007.1] in exon 3 of the AP1S2 gene
related to Pettigrew syndrome and the mother was found to be heterozygous for the same variant. Though
hydrocephalus and DWM are etiologically heterogeneous, AP1S2 gene-related Pettigrew syndrome should be
considered in individuals who are found to have these intracranial anomalies with autism and intellectual
disability.
Pettigrew syndrome is a rare X-linked intellectual developmental disorder (Cacciagli et al., 2014) with variable phenotypic
features. Global developmental delay, facial dysmorphism, and hydrocephalus are common findings of this disorder.
Dysmorphic features include macrocephaly/microcephaly, high forehead, anteverted large ears, strabismus, long nose, and
micrognathia. Behavioral abnormalities, autism, and abnormal gait have been reported in some patients. Cerebral
calcification, iron deposition in basal ganglia, and choreoathetosis are uncommon findings. AP1S2 gene contains five exons
and codes for adaptor protein-1 (Baltes et al., 2014). AP1S2 gene pathogenic variants and their association with
Pettigrew syndrome were first identified in 2006. Till now only nine pathogenic variants have been identified in
the AP1S2 gene (Huo Let al., 2019). All these pathogenic variants are either nonsense variants or splice
variants.
3 Clinical report
Figure 1: Figure 1:Clinical photographs depicting the facial, radiological, and genetic characteristics of the child Figure 1A: Frontal and lateral view of the face showing dysmorphism in the form of a long face, depressed
metopic suture and supraorbital ridges, flat forehead, low-set left ear, long nose, and a short philtrum Figure 1B: MRI brain showing Dandy-Walker malformation Figure 1C: Targeted Sanger sequencing confirmed presence of the hemizygous variant c.286dup in exon 3 of the
AP1S2 gene in the child
This male child, referred at the age of 7.5 years for evaluation of global developmental delay, autism, and behavioral
disturbances, was born to a healthy non-consanguineous couple. The first and second pregnancies of the couple resulted in
spontaneous abortions and one pregnancy was terminated due to unilateral hydrocephalus in the fetus. The boy was born
by vaginal delivery with a birth weight of 3.5 kg. There was no history suggestive of teratogenic exposures or maternal
comorbidities. The nuchal scan and detailed fetal anomaly scan were normal. A growth scan at 9 months of gestation
revealed hydrocephalus (ventricular atrial diameter of 17 mm) in the fetus. Postnatally, ventriculoperitoneal (VP) shunt
placement was done for hydrocephalus at the age of 3 months. There was no feeding difficulty or respiratory distress. The
child had global developmental delay and autism and was not able to speak. He had not attained bladder and
bowel control. There were no seizures or visual abnormalities. Hearing was impaired as per the parents.
The mother was pregnant again and had been referred at around 8 weeks of gestation for prenatal genetic
counselling.
On examination of the child, the head circumference was 48.5 cm (5th-10th centile), height was 122 cm
(50th centile), and weight was 21 kg (25th-50th centile). There was craniofacial dysmorphism in the form of
plagiocephaly, long face, depressed metopic suture and supraorbital ridges, flat forehead, low set left ear,
long nose, and short philtrum (Figure 1A). The neck, chest, spine, and extremities were normal. The feet
were flat. The child was not responding to sounds and there was no eye contact. There was hypotonia
with normal deep tendon reflexes. Examination of other systems was normal. MRI brain was suggestive of
communicating hydrocephalus with a Dandy-Walker malformation (Figure 1B). The electroencephalogram
(EEG) was normal. The couple was counseled regarding the possibility of a genetic etiology. Differentials
considered were either a copy number variation or a neurodevelopmental disorder with structural brain
abnormalities.
Figure 2: Pathogenic variants reported in the AP1S2 gene; the variant identified in our patient is shown in red
font
Chromosomal microarray of the boy did not reveal any clinically significant copy number variants. Trio whole-exome
sequencing (WES) revealed a novel hemizygous pathogenic variant (PM2, PVS1, PP3, PP4) c.286dup (p.Ser96LysfsTer4)
[NM_001369007.1] in exon 3 of AP1S2 gene related to Pettigrew syndrome. Targeted Sanger sequencing confirmed
presence of the variant in hemizygous form in the child (Figure 1C) and revealed heterozygosity for the variant in the
mother. The couple was counselled regarding the X-linked recessive inheritance of the disorder with a 50% risk of
recurrence in each male offspring. They opted for prenatal genetic testing of the ongoing pregnancy and amniocentesis was
done. Targeted testing of the AP1S2 gene variant in the amniocyte DNA revealed absence of the variant in the
fetus.
4 Discussion
In 1973, Fried and Sanger first reported a Scottish family with X-linked mental retardation with hydrocephalus (Fried &
Sanger, 1973). Later, multiple individuals with intellectual disability and Dandy-Walker malformation (DWM)
with or without hydrocephalus were categorized under X-linked intellectual disability disorder and the
condition was named Pettigrew syndrome (PGS) (Pettigrew et al., 1991; Cowles et al., 1993; Carpenter et al.,
1999; Turner et al., 2003; Wakeling et al., 2002). AP1S2 gene pathogenic variants and their association
with Pettigrew syndrome were first identified in 2006 in families with intellectual disability and abnormal
behaviour (Tarpey et al., 2006). Basal ganglia calcification is also one of the requisite findings to recognize
this syndrome (Saillour et al., 2007; Borck et al., 2008; Cacciagli et al., 2014). Till now, there are only 58
patients who have been diagnosed with PGS caused by AP1S2 mutation. Intrafamilial and interfamilial
variable expressivity has been observed. Though facial dysmorphism is seen in many cases with PGS there
are no specific dysmorphic features. Macrocephaly, long face, high forehead, protruding ears, strabismus,
long nose, and small pointed jaw are some of the common facial features reported with PGS (Huo et al.,
2019).
Imaging features of the brain may be normal in early childhood or affected individuals may have hydrocephalus,
cerebellar/ posterior fossa anomalies (Strain et al., 1997), and/or iron and calcium depositions in the basal ganglia.
Periventricular nodular heterotopia has also been reported. Based on imaging and brain pathology in Pettigrew syndrome,
neurodegeneration begins with iron deposition. Serial imaging of the brain would be required to identify the same. Table 1
compares the clinical features in previously reported cases and our case. Female carriers are usually asymptomatic. Mild
intellectual disability and iron deposition with neuroaxonal dystrophy in the basal ganglia leading to presenile dementia
have been reported in a few carrier females. This could be due to skewed X inactivation (Pettigrew et al.,
1991).
AP1S2 gene has 5 exons and encodes the sigma-2 subunit of the heterotetrameric adaptor protein-1 (AP1) and
plays a role in the assembly of endocytic vesicles and recognition of signals of transmembrane receptors
(Baltes et al., 2014; Glyvuk et al., 2010). Till now 9 pathogenic loss-of-function variants (5 intronic variants
and 4 exonic variants) have been reported (Figure 2). The variant identified in our patient is a novel
variant. Intrafamilial and interfamilial variable expressivity are not explained by the type of pathogenic
variants. Genotype-phenotype correlations are not well defined in this syndrome as there are only a few cases
reported till now. Based on previous reports, those with nonsense mutations had a higher incidence of
microcephaly; seizures were common in cases with splice site mutations. Our patient did not have microcephaly or
seizures.
The recurrence risk estimation is by exact molecular diagnosis and carrier status of the mother. In our case as the
mother was a carrier, the recurrence risk was 50% for each male offspring. If the mother is not a carrier for the disorder,
the empiric recurrence risk due to gonadal mosaicism is not more than 1%. Preimplantation genetic diagnosis
and assisted reproduction with use of donor ovum (for female carriers) are other available reproductive
options.
Table 1: Comparison of the clinical features of previously reported individuals with Pettigrew syndrome with
those of our patient
Clinical feature/finding
n-58 (% of previously reported patients)
Our patient
Motor developmental delay
59%
+
Intellectual disability
100%
+
Autism
7%
+
Seizures
82%
-
Aggressive behaviour
52%
-
Self–abusive behavior
48%
-
Facial dysmorphism
52%
+
Microcephaly
72%
-
Hypotonia
53%
+
Abnormal gait
26%
-
Hydrocephalus
76%
+
Dandy-Walker malformation
17%
+
Cerebral calcification
12%
-
Iron deposition in basal ganglia
9%
-
5 Conclusion
This case highlights that AP1S2-related Pettigrew syndrome, though a rare cause of X-linked intellectual disability,
should be considered in cases with prenatal presentation of hydrocephalus and Dandy-Walker malformation, and
postnatal presentation with autism and intellectual disability.
6 Acknowledgments
The authors wish to thank the patient and family for their cooperation and for giving consent for photography.
References
1. Baltes J, et al. σ1B adaptin regulates adipogenesis by mediating the sorting of sortilin in adipose tissue. J
Cell Sci. 2014; 127(Pt16): 3477–3487.
2. Borck G, et al. Clinical, cellular, and neuropathological consequences of AP1S2 mutations: Further
delineation of a recognizable X–linked mental retardation syndrome. Hum Mutat. 2008; 29(7): 966–974.
3. Cacciagli P, et al. AP1S2 is mutated in X–linked Dandy-Walker malformation with intellectual disability,
basal ganglia disease, and seizures (Pettigrew syndrome). Eur J Hum Genet. 2014; 22(3): 363–368.
4. Carpenter NJ, et al. Regional localization of a nonspecific X-linked mental retardation gene (MRX59) to
Xp21.2-p22.2. Am J Med Genet. 1999; 85: 266–270.
5. Cowles T, et al. Prenatal diagnosis of Dandy-Walker malformation in a family displaying X-linked
inheritance. Prenat Diag. 1993; 13: 87–91.
6. Fried K, Sanger R. Possible linkage between Xg and the locus for a gene causing mental retardation with
or without hydrocephalus. J Med Genet. 1973; 10: 17–18.
7. Glyvuk N, et al. AP–1/sigma1B-adaptin mediates endosomal synaptic vesicle recycling, learning, and
memory. EMBO Journal. 2010; 29(8): 1318–1330.
8. Huo L, et al. A novel splice site mutation in AP1S2 gene for X–linked mental retardation in a Chinese
pedigree and literature review. Brain Behav. 2019; 9(3); e01221.
9. Pettigrew AL, et al. New X-linked mental retardation disorder with Dandy–Walker malformation, basal
ganglia disease, and seizures. Am J Med Genet. 1991; 38(2–3): 200–207.
10. Saillour Y, et al. Mutations in the AP1S2 gene encoding the sigma 2 subunit of the adaptor protein 1
complex are associated with syndromic X–linked mental retardation with hydrocephalus and calcifications in
basal ganglia. J Med Genet. 2007; 44(11): 739–744.
11. Strain L, et al. Fried syndrome is a distinct X-linked mental retardation syndrome mapping to Xp22. J
Med Genet. 1997; 34(7): 535–540.
12. Tarpey PS, et al. Raymond, mutations in the gene encoding the Sigma 2 subunit of the adaptor protein
1 complex, AP1S2, cause X–linked mental retardation. Am J Hum Genet. 2006; 79(6): 1119–1124.
13. Turner G, et al. Syndromic form of X–linked mental retardation with marked hypotonia in early life,
severe mental handicap, and difficult adult behavior maps to Xp22. Am J Med Genet. Part A. 2003; 117A (3):
245–250.
14. Wakeling EL, et al. X-linked inheritance of Dandy-Walker variant. Clin Dysmorphol. 2002; 11(1): 15-18.