A New Case of 13q12.2q13.1 Microdeletion Syndrome Contributes to Phenotype Delineation

A recently described genetic disorder has been associated with 13q12.3 microdeletion spanning three genes, namely, KATNAL1, LINC00426, and HMGB1. Here, we report a new case with similar clinical features that we have followed from birth to 5 years old. The child carried a complex rearrangement with a double translocation: 46,XX,t(7;13)(p15;q14),t(11;15)(q23;q22). Array-CGH identified a de novo microdeletion at 13q12.2q13.1 spanning 3–3.4 Mb and overlapping 13q12.3 critical region. Clinical features resembling those reported in the literature confirm the existence of a distinct 13q12.3 microdeletion syndrome and provide further evidence that is useful to characterize its phenotypic expression during the 5 years of development.


Introduction
Array-CGH has gained increased recognition as a first-tier technique to identify and characterize the genetic determinants of intellectual disability (ID) syndromes. Following its introduction, the detection rate of molecular cytogenetic alterations has increased by up to 15% in unselected patients with ID [1,2]. The possibility of comparing patient phenotypes with overlapping rearrangements has led to the identification of several novel microdeletion/microduplication syndromes [2]. A 13q12.3 microdeletion syndrome has recently been described involving a ∼300 kb critical region spanning only three genes, namely, KATNAL1, HMGB1, and the noncoding RNA LINC00426 [3].
Here, we describe a Caucasian patient with a de novo complex chromosomal rearrangement [t(7;13) and t(11;15)] including a 3-3.4 Mb microdeletion on 13q12.2q13.1, overlapping with the 13q12.3 microdeletion syndrome region. This subject displays the characteristic dysmorphic features highlighted in the recently reported cases, as well as psychomotor developmental delay and markedly delayed speech.

Clinical Report
The proband was the third daughter of a 41-year-old mother and a 42-year-old father. Both parents and siblings were healthy. Prenatal ultrasounds did not reveal any foetal malformations. Prenatal karyotype analysis by standard GTG banding, performed due to advanced maternal age, showed a de novo double translocation [46,XX,t(7;13) (p15;q14),t(11;15)(q23;q22)] (Figure 1(a)); UPD was ruled out for chromosomes 7, 11, and 15. Birth occurred through elective caesarean section at the 38th week of gestation (APGAR 7/8). Birth parameters were at the 50th centile according to the Italian growth curves (length: 50 cm (50th cent); weight: 2.79 kg (50th cent); head circumference: 34.5 cm (50th cent)).  We excluded cerebral malformations by brain ultrasound analysis and ocular defects by carrying out a fundus oculi exam. ECG examination showed a long QT (QTc: 470 ms), which was not reconfirmed at 17 days. Dysmorphisms included large wide set eyes, long philtrum, thin upper lip, and large ears ( Figure 2). An angioma was present on the thorax and another was found on the top of the head.
From infancy to the last follow-up at 5 years old, growth parameters were consistently below target levels. At 5 years, the measured parameters of the child were as follows: height: 100 cm (3rd cent); weight: 13 kg (<3rd cent/−2.8 SD); head circumference: 49 cm (10th cent). She displayed psychomotor delay: at 8 months she was unable to sit unsupported and at 18 months, after physiotherapy treatment, she still required support for walking. Lallation began at 16 months and language development was markedly impaired (at 5 years she pronounced very few words that included phonological alterations). The Griffiths test performed at 20 months old revealed a mental age of 14.4 months.
Examination at 2 years old revealed a normal EEG but brain MRI showed mild hypomyelination of the subcortical regions and thinning of the corpus callosum. Urinary and plasmatic aminoacid screenings were normal.
Postnatal array-CGH 44 K (Agilent, Santa Clara, CA) performed at 1 year old identified a 3-3.4 Mb microdeletion on chromosome 13q12.2q13.1, close to the translocation breakpoint on chromosome 13 (Figure 1(b)). The deletion was shown to span from position 28,963,865 to 31,955,272 Case Reports in Genetics  (minimal region) (NCBI Build 37/hg19), to contain 20 transcripts (15 coding genes), and did not overlap with common copy number variants (Database of Genomic Variants, http://projects.tcag.ca/variation/) (Figure 1(c)). The deletion was confirmed by real-time quantitative PCR assay designed to target exon 4 of the microtubule-associated tumour suppressor candidate 2 gene (MTUS2, NM 001033602.2). The same assay was used to confirm the de novo origin of this rearrangement.

Discussion
The 13q12.3 microdeletion syndrome was recently described in three patients presenting with intellectual disability, microcephaly, and eczema/atopic dermatitis [3]. Here, we describe a fourth patient with strikingly similar dysmorphic features, confirming the presence of a recognizable phenotype. Common clinical features included reduced head circumference, triangular face, high frontal hairline, large ears, wide set eyes, fullness of eyelids, malar flattening, a prominent nose with underdeveloped alae nasi and low insertion columella, thin upper lip vermilion, and a pointed chin. Our patient had one episode of cutaneous rash, but a specific diagnosis of atopic dermatitis was not made. All patients have shown delayed speech development and moderate intellectual deficit. In three out of four patients recurrent upper airway respiratory infections were reported. Other features shared by the described patients (namely, recurrent vomiting, failure to thrive, allergies, abnormal vision, oligodontia, or truncal obesity) were not observed in our proband.
Several other deletions and duplications that partially or totally overlap the present one, which are associated with a particular phenotype, are reported in the Decipher database (https://decipher.sanger.ac.uk/) (Figure 1(c) and Table 1). In particular, four deletions are partially or totally included in the deletion of this case study (DECIPHER cases numbers 249924, 282282, 4587, 266456, and 279188) and these patients show intellectual disability, language delay, microcephaly, and facial dysmorphisms. Moreover, behavioural abnormalities similar to the ones described by Bartholdi et al. were reported in two cases ( Table 1). The minimal shared region between these deletions and the deletion reported in our patient includes the three genes KATNAL1 (MIM 614764), LOC100188949, and HMGB1 (MIM 163905) [3]. A causal role can be easily suggested for HMGB1 only, which encodes a ubiquitous nonhistone chromosomal protein expressed in brain (Allen Mouse Brain Atlas, http://mouse.brain-map.org/). This is a possible dosagesensitive gene involved in the inflammatory response that may contribute to neuronal excitability and seizures [4,5].