15q24 microdeletion syndrome
The phenotype of the 15q24 deletion is heterogeneous, but all 14 cases described to date (including the present case) have intellectual disability ranging from mild to severe, and characteristic facial features (Table 1; Additional File 2), suggesting that the 15q24 deletion phenotype may be clinically recognizable . Facial characteristics include high anterior hairline, broad medial eyebrows, hypertelorism, downslanted palpebral fissures, epicanthus, long and smooth philtrum, full lower lip and abnormal ears. Other common features include minor digital anomalies (85%), impaired speech development (80%), genital abnormalities in males (73%), hypotonia (69%), eye abnormalities such as strabismus and nystagmus (62%), joint laxity (62%) and recurrent infections (54%). Less commonly reported features include low birth weight, growth hormone deficiency, diaphragmatic and inguinal hernias, scoliosis and other musculoskeletal abnormalities, bowel atresia, hearing loss and major central nervous system abnormalities (dysplastic corpus callosum with a transected pituitary stalk, myelomeningocele with hydrocephalus and multiple cysts of the corpus callosum) [2, 3, 6].
In this study, we detected a 3.06 Mb de novo deletion of 15q24 of paternal origin in a boy with overlapping clinical features with the previously reported cases of 15q24 microdeletion, including low birth weight, developmental delay, distinct facial features, digital, eye and ear abnormalities, severely impaired language, joint laxity, scoliosis and recurrent respiratory infections. The association with nystagmus is in agreement with an earlier report . Although hypotonia had never been described in the present case, he had delayed motor development, did not walk independently until 30 months and received physical therapy for 4 years, suggesting that he might have been mildly hypotonic. Our patient had no genital abnormalities, whereas hypospadias, micropenis or crytoptorchism have been reported in 8 of 10 previously reported males [2–6].
In addition, patient AU008 exhibited classic features of autism, along with constant smiling and inappropriate laughter, reminiscent of Angelman syndrome. Of the four male cases with a microdeletion of 15q24 initially reported by Sharp et al., three were noted to have happy facial expressions, whereas the fourth subject was described as having 'autistiform' traits . Review of the literature identified two other patients with ASD carrying 15q24 deletions, thus adding this microdeletion syndrome to the increasing list of rare genomic disorders involved in the etiology of autism. Smith et al. described a girl with autism carrying an interstitial deletion of chromosome 15q originally mapped by FISH to 15q22-q23 . However, a recent reassessment of this patient using Affymetrix SNP 6.0 microarrays identified a 3.12 Mb deletion (70.740-73.860 Mb) between LCR15q24A and 15q24D (Moyra Smith, personal communication). The girl's phenotype was very similar to that observed in our patient; both exhibited classic autism, intellectual disability, delayed motor development and mild dysmorphic facial features. In addition, both had language regression and were nonverbal at the time of evaluation, they showed prominent mouthing behavior and they had frequent infections. The second patient with ASD carrying a 15q24 microdeletion was identified by Marshall et al. in a whole-genome CNV analysis, and limited clinical information was provided . This child appeared to have a more severe phenotype, with severe dysmorphism, severe scoliosis and diaphragmatic hernia (see Additional File 2). The real frequency of ASD among 15q24 deletion carriers is unknown, as the majority of patients reported to date were not formally evaluated for autism. The fact that only some patients with 15q24 deletion have ASD is similar to observations in many other microdeletion and microduplication syndromes, and is part of the variable clinical presentation that can be observed in these genomic disorders. Examples of where ASD can be part of the phenotype at varying rates include 15q11-q13 duplication, 22q13 deletion, Angelman, DiGeorge, Potocki-Lupski and Williams syndromes, to name but a few [17, 18]. Other behavioral traits reported in 15q24 deletions include hyperactivity/attention deficit-hyperactivity disorder in two patients, aggressiveness in two and sleep difficulties in one, suggesting that this deletion may confer susceptibility to other neuropsychiatric disorders.
Although it is difficult to perform detailed genotype-phenotype correlations given the limited number of patients described to date, some observations are beginning to emerge. Notably, of the 14 cases with deletions of chromosome 15q24, 12 are males [2–6, 8, 9]. This distortion in the sex ratio raises the possibility that the penetrance may be influenced by the sex of the individual. Although the phenotype in the two females [3, 8] does not appear to differ significantly from that observed in males (see Additional File 2), the apparently biased sex ratio is intriguing, and needs to be confirmed as additional patients are reported. Diaphragmatic hernia has been described in three patients with deletions involving the LCR15q24A-15q24B interval [2, 5, 9], but was not observed in patient AU008 or in four other patients with deletions affecting the same interval [3, 6, 8], suggesting incomplete penetrance.
Frequency of 15q24 microdeletions in ASD
In our study of the Costa Rican sample, we observed one case of 15q24 microdeletion syndrome in 173 unrelated cases ascertained for ASDs. This corresponds to a frequency of 0.54%. This compares to a frequency of 0.23% (1/427) in the study of Marshall et al. and a frequency of 0% (0/785 unrelated cases) in the AGRE families. Combining these studies results in an overall frequency of 15q24 microdeletions in patients ascertained for ASD of 0.14% (2/1385). It should be noted that both the AGRE cohort  and the Canadian cohort  included large proportions of multiplex families (63% and 44%, respectively). Given that in all cases where parental samples were available, 15q24 microdeletions have been shown to be de novo, it is likely that rates are higher in simplex families, thus, the rate of 0.14% should be considered as a lower bound. The rates observed in samples ascertained for ASD were in the same order of 15q24 microdeletions observed in patients ascertained for unexplained intellectual disability and congenital anomalies (~0.33%; 4/1200) .
Parental origin of 15q24 deletions
In the three cases with ASD reported to date, the deletion arose in the paternal chromosome (the present case; the girl described by Smith et al. (Moyra Smith, personal communication) and the case reported by Marshall et al.). By contrast, three of the subjects described by Sharp et al. (two with happy facial expression and one with autistic traits), carried deletions of maternal origin. Parental origin was not determined in the remaining cases. It is thus unclear at present the relevance, if any, of the gender of the parent of origin to the resultant behavioral phenotype, and more information is needed. However, it should be noted that no imprinted genes have been described in the deleted 15q23-q24 interval http://www.geneimprint.com/.
Atypical 15q24 microdeletion breakpoints
Breakpoints of the 15q24 microdeletions described to date are typically defined by segmental duplications, which predispose to recurrent chromosomal rearrangements via non-allelic homologous recombination [2–6]. However, both breakpoints in our patient lie outside these segmental duplications. Similarly, Marshall et al. reported a subject with ASD carrying a deletion of 15q23-q24.2, with the proximal breakpoint lying outside the segmental duplications and within the THSD4 gene, as in the patient described here (Figure 1), and extending distally to LCR15q24D. However, the breakpoints in THSD4 appear to be different, at 69.60 Mb (intron 6) in the subject described by Marshall et al. and at 69.84 Mb (intron 14) in patient AU0008. Finally, one of the patients described by Sharp et al. (IMR371) had an atypical 15q24 deletion (Figure 1), and precise mapping of both breakpoints and sequencing of the junction fragment revealed two unique breakpoints that were not located within repetitive sequences and had no apparent pairwise homology . The presence of atypical deletions provides an important opportunity to better understand the genes in the minimal region and their relationship to phenotype.
Genes in the minimal deletion interval
Despite the varying sizes of the 15q24 deletions reported, no correlation has been observed between the extent of the deletion and clinical severity [2–6, 8, 9]. In fact, the phenotypic similarities between all patients suggest that haploinsufficiency of one or several genes within the minimal deletion interval are responsible for the syndrome. The molecular characterization of the atypical deletion in patient AU008 provides a considerably reduced minimal deletion interval, from 1.75 Mb to 766 kb, implicating a reduced number of genes (15 versus 38 Refseq genes). Of these genes, two have been implicated in autosomal recessive disorders. Homozygous mutations in STRA6 result in a multiple malformation syndrome typically associated with anophthalmia or microphthalmia , the latter also observed in one patient with 15q24 deletion syndrome . CYP11A1 codes for the mitochondrial cholesterol side-chain cleavage enzyme (cytochrome P450scc), catalyzing the first step of steroid biosynthesis leading to production of glucocorticoids, mineralocorticoids and sex hormones. Homozygous mutations in this gene can lead to congenital adrenal insufficiency with disordered sexual differentiation .
In addition to CYP11A1, two other genes involved in metabolism, CYP1A1 and CYP1A2, are found in the minimal interval. These genes are involved in the metabolism of endogenous and xenobiotic compounds, including caffeine, theophylline, acetominophen, naproxen and many psychiatric drugs (see the updated list at the Indiana University Drug Interaction table http://medicine.iupui.edu/clinpharm/ddis/table.asp). Careful assessment of drug dosing and sensitivity is therefore warranted in 15q24 deletion carriers. As these enzymes are also important in the metabolism of xenobiotics including environmental toxins, both increased and decreased sensitivity to such toxins might be expected (see  for review).
Focusing on neural expressed genes, review of the Allen Brain Atlas http://www.brain-map.org expression data on these genes for four brain regions (cerebellum, CB; neocortex, CTX; hippocampal formation, HPF; and amygdala, AMY) shows very high and ubiquitous staining for UBL7 and region-specific, high levels of expression of SEMA7A (CB), ARID3B (CTX, HPF, AMY) and CLK3 (CTX, HPF) (see Additional File 3). Of these, SEMA7A (semaphorin 7A), is crucial for proper axon tract formation during embryonic development [22, 23] and T-cell-mediated immune function . SEMA7A binds to plexin-C1 and to integrin-β1 [25, 26]. There is evidence from knockout mice that the effects of SEMA7A in axon outgrowth are mediated by integrin-β1 and mitogen-activated protein kinase signaling pathways, possibly thereby regulating the actin cytoskeleton . Interestingly, another member of the semaphorin family, SEMA5A, was recently implicated in ASDs through gene expression studies  and genome-wide association studies .
Ingenuity pathway analysis confirmed significant association of genes in the minimal interval with several metabolic processes (drug metabolism, small molecule biochemistry, protein synthesis, lipid metabolism and vitamin and mineral metabolism; maximum P values 5.7 × 10-07 to 1.2 × 10-05) driven entirely by the three CYP-family genes. One interesting finding is that PRDM5, which is a zinc finger protein, binds to seven genes in the interval (GOLGA6, ISLR2, ISLR, CCDC33, UBL7, ARID3B and CLK3) and regulates their expression , indicating coordinated regulation of expression, in turn suggesting an as yet unidentified common functionality. Disruption of multiple genes in a common pathway is more likely to lead to observable phenotypes.