X-exome sequencing of 405 unresolved families identifies seven novel intellectual disability genes.

X-linked intellectual disability (XLID) is a clinically and genetically heterogeneous disorder. During the past two decades in excess of 100 X-chromosome ID genes have been identified. Yet, a large number of families mapping to the X-chromosome remained unresolved suggesting that more XLID genes or loci are yet to be identified. Here, we have investigated 405 unresolved families with XLID. We employed massively parallel sequencing of all X-chromosome exons in the index males. The majority of these males were previously tested negative for copy number variations and for mutations in a subset of known XLID genes by Sanger sequencing. In total, 745 X-chromosomal genes were screened. After stringent filtering, a total of 1297 non-recurrent exonic variants remained for prioritization. Co-segregation analysis of potential clinically relevant changes revealed that 80 families (20%) carried pathogenic variants in established XLID genes. In 19 families, we detected likely causative protein truncating and missense variants in 7 novel and validated XLID genes (CLCN4, CNKSR2, FRMPD4, KLHL15, LAS1L, RLIM and USP27X) and potentially deleterious variants in 2 novel candidate XLID genes (CDK16 and TAF1). We show that the CLCN4 and CNKSR2 variants impair protein functions as indicated by electrophysiological studies and altered differentiation of cultured primary neurons from Clcn4(-/-) mice or after mRNA knock-down. The newly identified and candidate XLID proteins belong to pathways and networks with established roles in cognitive function and intellectual disability in particular. We suggest that systematic sequencing of all X-chromosomal genes in a cohort of patients with genetic evidence for X-chromosome locus involvement may resolve up to 58% of Fragile X-negative cases.

Refinement of cortical dysgeneses spectrum associated with TUBA1A mutations.

OBJECTIVE: We have recently shown that de novo mutations in the TUBA1A gene are responsible for a wide spectrum of neuronal migration disorders. To better define the range of these abnormalities, we searched for additional mutations in a cohort of 100 patients with lissencephaly spectrum for whom no mutation was identified in DCX, LIS1 and ARX genes and compared these data to five previously described patients with TUBA1A mutations. RESULTS: We detected de novo TUBA1A mutations in six patients and highlight the existence of a prominent form of TUBA1A related lissencephaly. In four patients, the mutations identified, c.1190T>C (p.L397P), c.1265G>A (p.R422H), c.1264C>T (p.R422C), c.1306G>T (p.G436R), have not been reported before and in two others, the mutation corresponds to a recurrent missense mutation, c.790C>T (p.R264C), likely to be a hot spot of mutation. All together, it emerges that the TUBA1A related lissencephaly spectrum ranges from perisylvian pachygyria, in the less severe form, to posteriorly predominant pachygyria in the most severe, associated with dysgenesis of the anterior limb of the internal capsule and mild to severe cerebellar hypoplasia. When compared with a large series of lissencephaly of other origins (ILS17, ILSX or unknown origin), these features appear to be specific to TUBA1A related lissencephaly. In addition, TUBA1A mutated patients share a common clinical phenotype that consists of congenital microcephaly, mental retardation and diplegia/tetraplegia. CONCLUSIONS: Our data highlight the presence of consistent and specific abnormalities that should allow the differentiation of TUBA1A related lissencephalies from those related to LIS1, DCX and ARX genes.

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.

Fried syndrome, first described in 1972, is a rare X-linked mental retardation that has been mapped by linkage to Xp22. Clinical characteristics include mental retardation, mild facial dysmorphism, calcifications of basal ganglia and hydrocephalus. A large four-generation family in which the affected males have striking clinical features of Fried syndrome were investigated for linkage to X-chromosome markers; the results showed that the gene for this condition lies within the interval DXS7109-DXS7593 in Xp22.2. In total, 60 candidate genes located in this region, including AP1S2, which was recently shown to be involved in mental retardation, were screened for mutations. A mutation in the third intron of AP1S2 was found in all affected male subjects in this large French family. The mutation resulted in skipping of exon 3, predicting a protein with three novel amino-acids and with termination at codon 64. In addition, the first known large Scottish family affected by Fried syndrome was reinvestigated, and a new nonsense mutation, p.Gln66X, was found in exon 3. Using CT, both affected patients from the French family who were analysed had marked calcifications of the basal ganglia, as previously observed in the first Scottish family, suggesting that the presence of distinctive basal ganglia calcification is an essential parameter to recognise this syndromic disorder. It may be possible to use this feature to identify families with X-linked mental retardation that should be screened for mutations in AP1S2.

[Epileptogenic brain malformations: radiological and clinical presentation and indications for genetic testing]. / Malformations cérébrales et épilepsie: présentations radiocliniques et implications pour le diagnostic génétique.

Malformations of cortical development (MCD) represent a major cause of developmental disabilities and severe epilepsy. Advances in imaging and genetics have improved the diagnosis and classification of these conditions. Up to now, eight genes have been involved in different types of MCD. Lissencephaly-pachygyria and subcortical band heterotopia (SBH) represent a malformative spectrum resulting from mutations of either LIS1 or DCX genes. LIS1 mutations cause a more severe malformation in the posterior brain regions. DCX mutations usually cause anteriorly predominant lissencephaly in males and SBH in female patients. Additional forms are X-linked lissencephaly with corpus callosum agenesis and ambiguous genitalia associated with mutations of the ARX gene. Lissencephaly with cerebellar hypoplasia (LCH) encompass heterogeneous disorders named LCH type a to d. LCHa are related with mutation in LIS1 or DCX, LCHb with mutation of RELN gene, and LCHd could be related with TUBA1A gene. Polymicrogyria encompass a wide range of clinical, aetiological and histological findings. Among several syndromes, recessive bilateral fronto-parietal polymicrogyria has been associated with mutations of the GPR56 gene. Bilateral perisylvian polymicrogyria showed a linkage to chromosome Xq28 in some pedigrees, and mutations in SRPX2 gene in others conditions. X-linked bilateral periventricular nodular heterotopia (BPNH) consists of BPNH with focal epilepsy in females and prenatal lethality in males. Filamin A (FLNA) mutations have been reported in some families and in sporadic patients. It is possible to infer the most likely causative gene by brain imaging studies and other clinical findings. Based on this experience, a detailed phenotype analysis is needed to develop the most efficient research on MCD in the future.

Oligophrenin 1 mutations frequently cause X-linked mental retardation with cerebellar hypoplasia.

BACKGROUND: Mutations of oligophrenin 1, one of the first genes identified in nonspecific X-linked mental retardation (MRX), have been described in patients with moderate to severe cognitive impairment and predominant cerebellar hypoplasia, in the vermis. OBJECTIVE: To further delineate the phenotypic and mutational spectrum of the syndrome, by screening oligophrenin 1 in two cohorts of male patients with mental retardation (MR) with or without known posterior fossa anomalies. METHODS: Clinical examination, cognitive testing, MRI studies, and mutational analysis (denaturing gradient gel electrophoresis and direct sequencing) on blood lymphocytes were performed in 213 unrelated affected individuals: 196 patients classified as MRX and 17 patients with MR and previously detected cerebellar anomalies. RESULTS: Four novel oligophrenin 1 mutations were identified. In the MRX group, two nonsense mutations were detected. In the MR group, two mutations were found: a deletion of exons 16 to 17 and a splice site mutation. All patients shared characteristic clinical, radiologic, and distinctive features with a degree of intrafamilial variability in motor and cognitive deficits. CONCLUSIONS: Oligophrenin 1 mutations were found in 12% (2/17) of individuals with mental retardatin and known cerebellar anomalies and in 1% (2/196) of the X-linked mental retardation group.

First-trimester prenatal diagnosis of mucolipidosis II (I-cell disease) by chorionic biopsy.

We investigated the possibility of mucolipidosis type II (ML II) prenatal diagnosis by lysosomal enzyme determination on trophoblast biopsy obtained at 10 weeks of gestation in two pregnancies at risk. Diagnosis of ML II was made in both cases on fresh chorionic villi on the basis of depressed beta-galactosidase activity, and after abortion, the diagnosis was confirmed on fresh fetal tissues and on cells cultured from trophoblast and fetuses. We stress the importance of culturing cells from the trophoblast biopsy to ensure a reliable diagnosis.

Prenatal diagnosis of glycogenosis type II (Pompe's disease) using chorionic villi biopsy.

Glycogenosis type II (Pompe's disease) has been diagnosed using cultured amniotic cells for several years. In this paper, we present three prenatal diagnoses based on chorionic villi biopsy in three families at risk for Pompe's disease juvenile form: a normal fetus that was diagnosed and confirmed by enzymatic assay on amniotic cells; two affected fetuses that were diagnosed and confirmed on post-abortion fetal tissues. In one case a residual acid alpha-glucosidase activity was found; we concluded that the residual activity was due to maternal contamination. Prenatal diagnosis of Pompe's disease is therefore possible using chorionic villi biopsy.

Lysosomal hydrolase activity in chorionic villi and embryonic cells in culture.

Fourteen lysosomal enzymes were compared in 20 cultured cell lines from chorionic biopsy and corresponding embryonic tissue after voluntary abortions. Enzymatic expression appears to be similar in cultured cells from both sources with some slightly higher levels for chorionic villi. We stress the importance of culturing chorionic villi especially in the case of enzymes (alpha-L-iduronidase) or diseases (I cell disease) whose expression is unusual in fresh trophoblast tissue.

Prenatal diagnosis of a heterozygote for mucopolysaccharidosis type VII (beta-glucuronidase deficiency).

We had the opportunity of investigating a case (BK) of a severe form of mucopolysaccharidosis with nearly total deficiency of beta-glucuronidase in serum, leucocytes and fibroblasts. We here report results obtained by prenatal diagnosis of a clinically normal child (BK's sister), and point out the difficulty in interpreting a heterozygous level of beta-glucuronidase activity in cultured amniotic cells. Four successive passages of amniotic cells were tested for beta-glucuronidase and alpha-mannosidase activity in at-risk and control cells. In different passages, enzyme activity was between 8 and 49 per cent of controls but 2 to 18 times higher than fibroblasts from the affected brother (BK). The highest activity was observed in the first passage and the lowest in the third. The electrophoretic separation of GAGS from at-risk amniotic fluid showed a normal pattern. We discuss the correlation between enzyme levels in different passages of cultured cells and that found in leucocytes and fibroblasts from the propositus and parents. From a practical point of view, we conclude that the first passage gives the most reliable results for prenatal diagnosis.

A variant of mucolipidosis. II. Clinical, biochemical and pathological investigations.

We present in this paper a patient with a clinically intermediate form of mucolipidosis (ML). Lysosomal hydrolase activity in fibroblasts was normal and levels of these enzymes in culture media were not elevated. There was a striking elevation of several hydrolases in serum and a deficiency (15% of normal) of N-acetyl-glucosamine phosphotransferase in fibroblasts. Atypical electron microscopic findings were also observed. There was no evidence of increased synthesis, slower turnover, unbalanced distribution or further changes in lysosomal enzymes. Phosphotransferase deficiency against endogenous beta-glucosaminidase and the fact that the electrophoretic mobility of lysosomal enzymes was identical to that of MLII suggest that these enzymes are not phosphorylated. Hypotheses that could explain this atypical pathology are discussed.

First trimester prenatal diagnosis of metachromatic leukodystrophy on chorionic villi by 'immunoprecipitation-electrophoresis'.

Prenatal diagnosis of metachromatic leukodystrophy (MLD) due to arylsulphatase A (ASA) deficiency can be performed by amniocentesis with the disadvantage of a late pregnancy termination. Whether chorionic villi (CV) obtained by trophoblast biopsy during the first trimester of pregnancy can be useful for diagnosis depends on the reliability of results. The complexity of arylsulphatase expression in CV and the existence of several isozymes make diagnosis difficult. However, the use of an anti-ASA antiserum enabled us to discriminate between ASA and a comigrating contaminant isozyme, and the antigen-antibody (Ag-Ab) complex gave better evidence of the presence or absence of ASA after enhancement of activity with 4-methylumbelliferyl sulphate (4-MUS). We propose that immunoprecipitation followed by electrophoresis could be a valuable method of MLD prenatal diagnosis on chorionic villi.

Prenatal diagnosis of atypical Tay-Sachs disease by chorionic villi sampling.

We studied a family at risk for atypical TSD in which the index case showed, clinically, a late onset and a gradual psychomotor deterioration and biochemically, a residual hex. A activity in leucocytes. Two prenatal diagnoses of affected fetuses were made in this family. The first one on amniotic cells, the second one on trophoblast biopsy samples. Both of them were confirmed after abortion on cultured cells. Prenatal diagnosis of TSD, even of some atypical forms is possible using trophoblast biopsy, but formal confirmation should be obtained on cultured trophoblasts.