Barbara R. DuPont

Alterations in CDH15 and KIRREL3 in Patients with Mild to Severe Intellectual Disability

Cell-adhesion molecules play critical roles in brain development, as well as maintaining synaptic structure, function, and plasticity. Here we have found the disruption of two genes encoding putative cell-adhesion molecules, CDH15 (cadherin superfamily) and KIRREL3 (immunoglobulin superfamily), by a chromosomal translocation t(11;16) in a female patient with intellectual disability (ID). We screened coding regions of these two genes in a cohort of patients with ID and controls and identified four nonsynonymous CDH15 variants and three nonsynonymous KIRREL3 variants that appear rare and unique to ID. These variations altered highly conserved residues and were absent in more than 600 unrelated patients with ID and 800 control individuals. Furthermore, in vivo expression studies showed that three of the CDH15 variations adversely altered its ability to mediate cell-cell adhesion. We also show that in neuronal cells, human KIRREL3 colocalizes and interacts with the synaptic scaffolding protein, CASK, recently implicated in X-linked brain malformation and ID. Taken together, our data suggest that alterations in CDH15 and KIRREL3, either alone or in combination with other factors, could play a role in phenotypic expression of ID in some patients.

Association between deletion size and important phenotypes expands the genomic region of interest in Phelan–McDermid syndrome (22q13 deletion syndrome)

Background The clinical features of Phelan–McDermid syndrome (also known as 22q13 deletion syndrome) are highly variable and include hypotonia, speech and other developmental delays, autistic traits and mildly dysmorphic features. Patient deletion sizes are also highly variable, prompting this genotype–phenotype association study. Methods Terminal deletion breakpoints were identified for 71 individuals in a patient cohort using a custom-designed high-resolution oligonucleotide array comparative genomic hybridisation platform with a resolution of 100 bp. Results Patient deletion sizes were highly variable, ranging from 0.22 to 9.22 Mb, and no common breakpoint was observed. SHANK3, the major candidate gene for the neurologic features of the syndrome, was deleted in all cases. Sixteen features (neonatal hypotonia, neonatal hyporeflexia, neonatal feeding problems, speech/language delay, delayed age at crawling, delayed age at walking, severity of developmental delay, male genital anomalies, dysplastic toenails, large or fleshy hands, macrocephaly, tall stature, facial asymmetry, full brow, atypical reflexes and dolichocephaly) were found to be significantly associated with larger deletion sizes, suggesting the role of additional genes or regulatory regions proximal to SHANK3. Individuals with autism spectrum disorders (ASDs) were found to have smaller deletion sizes (median deletion size of 3.39 Mb) than those without ASDs (median deletion size 6.03 Mb, p=0.0144). This may reflect the difficulty in diagnosing ASDs in individuals with severe developmental delay. Conclusions This genotype–phenotype analysis explains some of the phenotypic variability in the syndrome and identifies new genomic regions with a high likelihood for causing important developmental phenotypes such as speech delay.

Disruption of the IL1RAPL1 gene associated with a pericentromeric inversion of the X chromosome in a patient with mental retardation and autism

To the Editor: Defects in a number of genes distributed on the human X chromosome have been associated with mental retardation (MR) and developmental delay (DD) (1–3). We have evaluated a 7-yearold boy with global DD, autism, facial dysmorphism and a pericentromeric inversion of the X chromosome. The patient was a full-term infant born to a 25-year-old female with mild MR (Fig. 1a). At age 7 years 9 months, the patient’s weight was 23 kg (30th centile), his height was 125 cm (40th centile) and his head circumference was 51 cm (20th centile). He had a frontal hair upsweep, increased inner canthal measurement (98th centile) and outer canthal measurement (97th centile), mildly upslanted palpebral fissures, thickened ears with upturned lobes, and a short nose with thickening of the alae nasi and columella (Fig. 1b). His midface gave a hypotonic appearance with an open mouth and tented upper lip. The lower teeth were crowded anteriorly. Diminished muscle tone with low strength was noted. He also had hyperreflexia of the lower limb but no clonus. On the Autism Diagnostic Observation Scale (ADOS) and the Childhood Autism Rating Scale, the patient scored well within the autism range [http://www.agre.org/ and (4)]. He received a composite score of 31 on the Vineland Adaptive Behavior Scale (Interview Edition), indicative of marked impairment. The patient’s mother experienced a severe varicella infection and associated fever, a seizure, and cerebrospinal fluid pleocytosis in infancy. She had an intelligence quotient of 69. Among the areas assessed, she had greater difficulty with reception and expression of verbal skills. She has also been diagnosed as having autism spectrum disorder using the ADOS. The patient’s grandmother was reported to be clinically normal. Routine chromosome analysis in the patient and his mother showed 46,Y,inv(X)(p22.1q13) and 46,X,inv(X)(p22.1q13) karyotypes, respectively (Fig. 1a). Grandmother had a normal 46, XX karyotype. X-inactivation studies showed a random X-inactivation pattern for both women (Fig. 1a). We mapped the Xp breakpoint to within the IL1RAPL1 gene in the patient and his mother. Clone RP4-653H3, containing exon 3 and the flanking introns of the IL1RAPL1 gene, spanned the Xp22.1 breakpoint (Fig. 1c–e). Southern blot analysis with a cDNA probe spanning exons 3 and 4 of IL1RAPL1 gave a normal restriction pattern in the patient (data not shown). Thus, the Xp breakpoint was inferred to lie in intron 2 of IL1RAPL1, a region of approximately 60 kb upstream of exon 3. The Xq13 inversion breakpoint was mapped between two clones, RP11-580P8 and RP11402P6 (Fig. 1g). Southern hybridization analysis was performed using an ACRC cDNA probe (exons 2–8) and a probe containing the entire coding region of CXCR3. Both probes gave normal restriction patterns in the patient (data not shown). Furthermore, we amplified a genomic fragment covering approximately 13 kb between the exon 21 of OGT and exon 2 of ACRC in the patient (data not shown). Altogether, these results suggest that the Xq13 breakpoint is likely to be located in the 40 kb genomic region flanking the CXCR3 gene. The Xq13 breakpoint interval contains several known genes (OGT, ACRC, CXCR3, KIAA2001 and RPS4X) (Fig. 1g). Reverse transcriptase-polymerase chain reaction analysis detected no loss of expression of these genes in the patient (data not shown). IL1RAPL1 has previously been shown to be disrupted/deleted or mutated in some patients

Deletion of the Immunoglobulin Domain of IL1RAPL1 Results in Nonsyndromic X-Linked Intellectual Disability Associated With Behavioral Problems and Mild Dysmorphism

X‐Linked intellectual disability accounts for a significant fraction of males with cognitive impairment. Many of these males present with a non‐syndromic phenotype and presently mutations in 17 X‐linked genes are associated with these patients. Mutations in IL1RAPL1 have been found in multiple families with non‐syndromic X‐linked intellectual disability. All of the published mutations predict loss of function of the protein. We have identified an additional two families with deletions of a portion of the gene that give rise to cognitive impairment, as well as some behavioral problems and mild dysmorphism. Our clinical findings better delineate the phenotypic spectrum associated with IL1RAPL1 mutations.

22q13.2q13.32 genomic regions associated with severity of speech delay, developmental delay, and physical features in Phelan-McDermid syndrome

Purpose:Phelan–McDermid syndrome is a developmental disability syndrome with varying deletions of 22q13 and varying clinical severity. We tested the hypothesis that, in addition to loss of the telomeric gene SHANK3, specific genomic regions within 22q13 are associated with important clinical features.Methods:We used a customized oligo array comparative genomic hybridization of 22q12.3-terminus to obtain deletion breakpoints in a cohort of 70 patients with terminal 22q13 deletions. We used association and receiver operating characteristic statistical methods in a novel manner and also incorporated protein interaction networks to identify 22q13 genomic locations and genes associated with clinical features.Results:Specific genomic regions and candidate genes within 22q13.2q13.32 were associated with severity of speech/language delay, neonatal hypotonia, delayed age at walking, hair-pulling behaviors, male genital anomalies, dysplastic toenails, large/fleshy hands, macrocephaly, short and tall stature, facial asymmetry, and atypical reflexes. We also found regions suggestive of a negative association with autism spectrum disorders.Conclusion:This work advances the field of research beyond the observation of a correlation between deletion size and phenotype and identifies candidate 22q13 loci, and in some cases specific genes, associated with singular clinical features observed in Phelan–McDermid syndrome. Our statistical approach may be useful in genotype–phenotype analyses for other microdeletion or microduplication syndromes.Genet Med 2014:16(4):318–328.

17p13.3 microduplications are associated with split-hand/foot malformation and long-bone deficiency (SHFLD)

Split-hand/foot malformation with long-bone deficiency (SHFLD) is a relatively rare autosomal-dominant skeletal disorder, characterized by variable expressivity and incomplete penetrance. Although several chromosomal loci for SHFLD have been identified, the molecular basis and pathogenesis of most SHFLD cases are unknown. In this study we describe three unrelated kindreds, in which SHFLD segregated with distinct but overlapping duplications in 17p13.3, a region previously linked to SHFLD. In a large three-generation family, the disorder was found to segregate with a 254 kb microduplication; a second microduplication of 527 kb was identified in an affected female and her unaffected mother, and a 430 kb microduplication versus microtriplication was identified in three affected members of a multi-generational family. These findings, along with previously published data, suggest that one locus responsible for this form of SHFLD is located within a 173 kb overlapping critical region, and that the copy gains are incompletely penetrant.

Clinical Experience in the Evaluation of 30 Patients with a Prior Diagnosis of FG Syndrome

Background: FG syndrome (FGS) is an X-linked disorder characterised by mental retardation, hypotonia, particular dysmorphic facial features, broad thumbs and halluces, anal anomalies, constipation, and abnormalities of the corpus callosum. A behavioural phenotype of hyperactivity, affability, and excessive talkativeness is very frequent. The spectrum of clinical findings attributed to FGS has widened considerably since the initial description of the syndrome by Opitz and Kaveggia in 1974 and has resulted in clinical variability and genetic heterogeneity. In 2007, a recurrent R961W mutation in the MED12 gene at Xq13 was found to cause FGS in six families, including the original family described by Opitz and Kaveggia. The phenotype was highly consistent in all the R961W positive patients. Methods: In order to determine the prevalence of MED12 mutations in patients clinically diagnosed with FGS and to clarify the phenotypic spectrum of FGS, 30 individuals diagnosed previously with FGS were evaluated clinically and by MED12 sequencing. Results: The R961W mutation was identified in the only patient who had the typical phenotype previously associated with this mutation. The remaining 29 patients displayed a wide variety of features and were shown to be negative for mutations in the entire MED12 gene. A definite or possible alternative diagnosis was identified in 10 of these patients. Conclusion: This report illustrates the difficulty in making a clinical diagnosis of FGS given the broad spectrum of signs and symptoms that have been attributed to the syndrome. Individuals with a phenotype consistent with FGS require a thorough genetic evaluation including MED12 mutation analysis. Further genetic testing should be considered in those who test negative for a MED12 mutation to search for an alternative diagnosis.

Autism in two females with duplications involving Xp11.22–p11.23

We present two phenotypically similar females with Xp duplication who have autism and epilepsy. Case 1 is a 14‐year‐old Honduran female with autism and medically refractory complex partial, secondarily generalized epilepsy. Case 2 is a 3‐year‐old Austrian female with autism and medically refractory complex partial epilepsy. Both patients also share features of severe intellectual disability (case 1 has a developmental quotient of 23, case 2 has a developmental quotient of 42) and dysmorphic facial features. Autism was confirmed by thorough clinical evaluations and testing. Case 1 has a karyotype of 46,X,dup(X)(p11.2–p22.33) and a highly skewed X‐inactivation pattern (94:6). Brain magnetic resonance imaging (MRI) and electroencephalogram (EEG) were abnormal. Case 2 has a 5‐megabase duplication of Xp11.22–p11.23 on chromosome microarray analysis. The patient has a random X‐inactivation pattern (77:23). Brain MRI was normal, but EEG was abnormal. Both patients have duplications involving the Xp11.22–p11.23 region, indicating that this is an area of interest for future translational autism research.

First case of deletion of the faciogenital dysplasia 1 (FGD1) gene in a patient with Aarskog–Scott syndrome

Mutations within the faciogenital dysplasia 1 (FGD1) gene in individuals with clinical features of Aarskog-Scott syndrome (AAS) include missense mutations and insertions and deletions that result in frameshifts and premature terminations. Whole gene deletion and duplication represent other mutational possibilities not yet reported for FGD1 but known to exist for other genes such as MECP2. We report the first case of a boy with clinical features of AAS with deletion of FGD1 gene identified using an oligonucleotide-based X chromosome-specific microarray after attempts to generate amplicons for all of the FGD1 coding exons failed and BAC microarray analysis showed no abnormality.

Prevalence of aneuploidies in South Carolina in the 1990s

Purpose: Folate insufficiency due to nutritional deficiency or folate processing gene mutations has been proposed as a trisomy 21 risk factor. This study examined the possibility that increased folic acid intake among women of childbearing age may decrease the prevalence of trisomy 21 and other aneuploidies.Methods: The prevalence of aneuploidies from 1990 through 1999 was compared with folic acid use in women of childbearing age in South Carolina.Results: Folic acid use and the prevalence of all aneuploidies significantly increased during this period.Conclusion: Increased folic acid utilization in South Carolina was not associated with decreased prevalence of trisomy 21 or other aneuploidies.