A specific mutation in TBL1XR1 causes Pierpont syndrome.

BACKGROUND: The combination of developmental delay, facial characteristics, hearing loss and abnormal fat distribution in the distal limbs is known as Pierpont syndrome. The aim of the present study was to detect and study the cause of Pierpont syndrome. METHODS: We used whole-exome sequencing to analyse four unrelated individuals with Pierpont syndrome, and Sanger sequencing in two other unrelated affected individuals. Expression of mRNA of the wild-type candidate gene was analysed in human postmortem brain specimens, adipose tissue, muscle and liver. Expression of RNA in lymphocytes in patients and controls was additionally analysed. The variant protein was expressed in, and purified from, HEK293 cells to assess its effect on protein folding and function. RESULTS: We identified a single heterozygous missense variant, c.1337A>G (p.Tyr446Cys), in transducin ß-like 1 X-linked receptor 1 (TBL1XR1) as disease-causing in all patients. TBL1XR1 mRNA expression was demonstrated in pituitary, hypothalamus, white and brown adipose tissue, muscle and liver. mRNA expression is lower in lymphocytes of two patients compared with the four controls. The mutant TBL1XR1 protein assembled correctly into the nuclear receptor corepressor (NCoR)/ silencing mediator for retinoid and thyroid receptors (SMRT) complex, suggesting a dominant-negative mechanism. This contrasts with loss-of-function germline TBL1XR1 deletions and other TBL1XR1 mutations that have been implicated in autism. However, autism is not present in individuals with Pierpont syndrome. CONCLUSIONS: This study identifies a specific TBL1XR1 mutation as the cause of Pierpont syndrome. Deletions and other mutations in TBL1XR1 can cause autism. The marked differences between Pierpont patients with the p.Tyr446Cys mutation and individuals with other mutations and whole gene deletions indicate a specific, but as yet unknown, disease mechanism of the TBL1XR1 p.Tyr446Cys mutation.

Kohlschütter-Tönz syndrome: mutations in ROGDI and evidence of genetic heterogeneity.

Kohlschütter-Tönz syndrome (KTS) is a rare autosomal recessive disorder characterized by amelogenesis imperfecta, psychomotor delay or regression and seizures starting early in childhood. KTS was established as a distinct clinical entity after the first report by Kohlschütter in 1974, and to date, only a total of 20 pedigrees have been reported. The genetic etiology of KTS remained elusive until recently when mutations in ROGDI were independently identified in three unrelated families and in five likely related Druze families. Herein, we report a clinical and genetic study of 10 KTS families. By using a combination of whole exome sequencing, linkage analysis, and Sanger sequencing, we identify novel homozygous or compound heterozygous ROGDI mutations in five families, all presenting with a typical KTS phenotype. The other families, mostly presenting with additional atypical features, were negative for ROGDI mutations, suggesting genetic heterogeneity of atypical forms of the disease.

A 3-base pair deletion, c.9711_9713del, in DMD results in intellectual disability without muscular dystrophy.

We have identified a deletion of 3 base pairs in the dystrophin gene (DMD), c.9711_9713del, in a family with nonspecific X-linked intellectual disability (ID) by sequencing of the exons of 86 known X-linked ID genes. This in-frame deletion results in the deletion of a single-amino-acid residue, Leu3238, in the brain-specific isoform Dp71 of dystrophin. Linkage analysis supported causality as the mutation was present in the 7.6 cM linkage interval on Xp22.11-Xp21.1 with a maximum positive LOD score of 2.41 (MRX85 locus). Molecular modeling predicts that the p.(Leu3238del) deletion results in the destabilization of the C-terminal domain of dystrophin and hence reduces the ability to interact with ß-dystroglycan. Correspondingly, Dp71 protein levels in lymphoblastoid cells from the index patient are 6.7-fold lower than those in control cell lines (P=0.08). Subsequent determination of the creatine kinase levels in blood of the index patient showed a mild but significant elevation in serum creatine kinase, which is in line with impaired dystrophin function. In conclusion, we have identified the first DMD mutation in Dp71 that results in ID without muscular dystrophy.

Practical guidelines for interpreting copy number gains detected by high-resolution array in routine diagnostics.

The correct interpretation of copy number gains in patients with developmental delay and multiple congenital anomalies is hampered by the large number of copy number variations (CNVs) encountered in healthy individuals. The variable phenotype associated with copy number gains makes interpretation even more difficult. Literature shows that inheritence, size and presence in healthy individuals are commonly used to decide whether a certain copy number gain is pathogenic, but no general consensus has been established. We aimed to develop guidelines for interpreting gains detected by array analysis using array CGH data of 300 patients analysed with the 105K Agilent oligo array in a diagnostic setting. We evaluated the guidelines in a second, independent, cohort of 300 patients. In the first 300 patients 797 gains of four or more adjacent oligonucleotides were observed. Of these, 45.4% were de novo and 54.6% were familial. In total, 94.8% of all de novo gains and 87.1% of all familial gains were concluded to be benign CNVs. Clinically relevant gains ranged from 288 to 7912 kb in size, and were significantly larger than benign gains and gains of unknown clinical relevance (P < 0.001). Our study showed that a threshold of 200 kb is acceptable in a clinical setting, whereas heritability does not exclude a pathogenic nature of a gain. Evaluation of the guidelines in the second cohort of 300 patients revealed that the interpretation guidelines were clear, easy to follow and efficient.

Balanced into array: genome-wide array analysis in 54 patients with an apparently balanced de novo chromosome rearrangement and a meta-analysis.

High-resolution genome-wide array analysis enables detailed screening for cryptic and submicroscopic imbalances of microscopically balanced de novo rearrangements in patients with developmental delay and/or congenital abnormalities. In this report, we added the results of genome-wide array analysis in 54 patients to data on 117 patients from seven other studies. A chromosome imbalance was detected in 37% of all patients with two-breakpoint rearrangements. In 49% of these patients, the imbalances were located in one or both breakpoint regions. Imbalances were more frequently (90%) found in complex rearrangements, with the majority (81%) having deletions in the breakpoint regions. The size of our own cohort enabled us to relate the presence of an imbalance to the clinical features of the patients by using a scoring system, the De Vries criteria, that indicates the complexity of the phenotype. The median De Vries score was significantly higher (P=0.002) in those patients with an imbalance (5, range 1-9) than in patients with a normal array result (3, range 0-7). This study provides accurate percentages of cryptic imbalances that can be detected by genome-wide array analysis in simple and complex de novo microscopically balanced chromosome rearrangements and confirms that these imbalances are more likely to occur in patients with a complex phenotype.

Bilateral polymicrogyria as the indicative feature in a child with a 22q11.2 deletion.

Polymicrogyria (PMG) is a brain malformation due to abnormal cortical organisation. It is a heterogeneous disorder associated with 22q11.2 deletion syndrome (also known as velocardiofacial (VCF) syndrome) amongst others. Since this association was first recognised in 1996, over 30 patients with PMG and 22q11.2 deletion have been described. In 22q11.2 deletion syndrome, PMG is mainly located in the perisylvian areas; it frequently has an asymmetrical presentation with a striking predisposition for the right hemisphere. Neurological features of perisylvian PMG include developmental delay/mental retardation, seizures, microcephaly, spasticity and oromotor dysfunction. Thus in children diagnosed with 22q11.2 deletion syndrome, a finding of PMG has important prognostic value. We present a seven-month old boy with microcephaly, short stature and developmental delay. A cerebral MRI showed slightly enlarged ventricles and symmetrical perisylvian polymicrogyria. A 22q11.2 deletion was revealed by array-based comparative genomic hybridization. Remarkably the boy had no other manifestations of VCF syndrome. Paediatricians, child neurologists and clinical geneticists should be aware that the presence of PMG (especially in the perisylvian areas) needs investigating for 22q11.2 deletion, even if other more common VCF syndrome features are absent.

Functional analysis of novel TBX5 T-box mutations associated with Holt-Oram syndrome.

AIMS: Holt-Oram syndrome (HOS) is a heart/hand syndrome clinically characterized by upper limb and cardiac malformations. Mutations in T-box transcription factor 5 (TBX5) underlie this syndrome, the majority of which lead to premature stops. In this study, we present our functional analyses of five (novel) missense TBX5 mutations identified in HOS patients, most of whom presented with severe cardiac malformations. METHODS AND RESULTS: Functional characterization of mutant proteins shows a dramatic loss of DNA-binding capacity, as well as diminished binding to known cardiac interaction partners NKX2-5 and GATA4. The disturbance of these interactions leads to a loss of function, as measured by the reduced activation of Nppa and FGF10 in rat heart derived cells, although with variable severity. Two out of the five mutations are peculiar: one, p.H220del, is associated with additional extra-cardiac defects, perhaps by interfering with other T-box dependant pathways, and another, p.I106V, leads to limb defects only, which is supported by its normal interaction with cardiac-specific interaction partners. CONCLUSION: Overall, our data are consistent with the hypothesis that these novel missense mutations in TBX5 lead to functional haploinsufficiency and result in a reduced transcriptional activation of target genes, which is likely central to the pathogenesis of HOS.

A 649 kb microduplication in 1p34.1, including POMGNT1, in a patient with microcephaly, coloboma and laryngomalacia; and a review of the literature.

We report on a male patient with intra-uterine growth retardation, microcephaly, coloboma, laryngomalacia and developmental delay. Array CGH analysis revealed a 649 kb duplication on chromosome 1p34.1. Only five patients with overlapping duplications have been reported thus far. Ten known genes are located in the duplicated region, including the POMGNT1 gene encoding for O-mannose beta-1,2-N-acetylglucosaminyltransferase. This gene, mutated in muscle-eye-brain disease, might be causative for the observed phenotype in our patient.

Nine patients with a microdeletion 15q11.2 between breakpoints 1 and 2 of the Prader-Willi critical region, possibly associated with behavioural disturbances.

Behavioural differences have been described in patients with type I deletions (between breakpoints 1 and 3 (BP1-BP3)) or type II deletions (between breakpoints 2 and 3) of the 15q11.2 Prader-Willi/Angelman region. The larger type I deletions appear to coincide with more severe behavioural problems (autism, ADHD, obsessive-compulsive disorder). The non-imprinted chromosomal segment between breakpoints 1 and 2 involves four highly conserved genes, TUBGCP5, NIPA1, NIPA2, and CYFIP1; the latter three are widely expressed in the central nervous system, while TUBGCP5 is expressed in the subthalamic nuclei. These genes might explain the more severe behavioural problems seen in type I deletions. We describe nine cases with a microdeletion at 15q11.2 between BP1-BP2, thus having a haploinsufficiency for TUBGCP5, NIPA1, NIPA2, and CYFIP1 without Prader-Willi/Angelman syndrome. The clinical significance of a pure BP1-BP2 microdeletion has been debated, however, our patients shared several clinical features, including delayed motor and speech development, dysmorphisms and behavioural problems (ADHD, autism, obsessive-compulsive behaviour). Although the deletion often appeared to be inherited from a normal or mildly affected parent, it was de novo in two cases and we did not find it in 350 healthy unrelated controls. Our results suggest a pathogenic nature for the BP1-BP2 microdeletion and, although there obviously is an incomplete penetrance, they support the existence of a novel microdeletion syndrome in 15q11.2.

Pigmentary mosaicism following the lines of Blaschko in a girl with a double aneuploidy mosaicism: (47,XX,+7/45,X).

We report on a 6-year-old girl with linear streaks of apparent hypopigmentation and hyperpigmentation following the Blaschko lines, growth retardation, bupthalmos of the left eye, and mild mental retardation. She had a 45,X karyotype in lymphocytes. In cultured fibroblasts a double aneuploidy mosaicism was detected, consisting of a cell line with trisomy for chromosome 7 and a cell line with monosomy for the X-chromosome and no cell line with a normal karyotype. Cutis tricolor or three levels of pigmentation in different skin areas suggested presence of a third, probably normal cell line. Double aneuploidy mosaicism of a cell line with monosomy X and a cell line with trisomy of an autosome is a rare finding. The combination of monosomy X with trisomy of chromosomes 8, 10, 13, 18, and 21 has been reported, but not the combination with trisomy 7. In the 45,X cell line, microsatellite analysis showed loss of the maternal X-chromosome, and presence of a maternal and paternal chromosome 7. The 47,XX,+7 cell line showed a paternal and a maternal X-chromosome, and a paternal and two identical maternal chromosomes 7. Mechanisms that might explain this double aneuploidy mosaicism are discussed.

Plantar lipomatosis, unusual facies, and developmental delay: confirmation of Pierpont syndrome.

In 1998, Pierpont et al. reported on two unrelated boys with plantar lipomatosis, unusual facial phenotype, and developmental delay as a possible new MR/MCA syndrome. Here we report on a 2-year-old boy with similar manifestations: axial hypotonia in the first few months, prolonged feeding problems, moderate developmental delay, no speech development, deep palmar and plantar grooves, fat pads at the anteromedial aspect of the heels, and a distinct facial phenotype (high forehead, high anterior hairline, mild midfacial hypoplasia, remarkably narrow and upward slanted palpebral fissures, broad nasal ridge and tip, broad philtrum, bowed upper lip, "pouting" lower lip, full cheeks, and flat occiput). Brain MRI and MR spectroscopy studies showed relatively small frontal lobes, some widening of the lateral and third ventricles, and increased choline levels in the frontal white matter. Cytogenetic studies in lymphocytes and skin fibroblasts and whole genome micro-array CGH failed to show abnormalities. The present patient has a phenotype almost identical to that of the earlier reported children (Pierpont et al. [1998]: Am J Med Genet 75:18-21), which thereby validates this as a separate MR/MCA syndrome, appropriately designated Pierpont syndrome. The cause of the entity remains uncertain, the most likely etiologies being X-linked recessive or autosomal dominant genes.

Toriello-Carey syndrome: delineation and review.

Toriello and Carey [1988: Am J Med Genet 31:17-23] first described a syndrome with component manifestations of corpus callosum agenesis, unusual facial appearance, Robin sequence, and other anomalies. This was termed the Toriello-Carey syndrome by Lacombe et al. [1992: Am J Med Genet 42:374-376]. Since then, 11 reports describing 16 additional children have been published; in addition, we have had the opportunity to review over 30 unpublished cases. However, for various reasons, only 25 of the unpublished patients were included in this review. Based on this total, we can begin to better delineate this syndrome, as well as provide some information on natural history.