De novo TBR1 variants cause a neurocognitive phenotype with ID and autistic traits:report of 25 new individuals and review of the literature

TBR1, a T-box transcription factor expressed in the cerebral cortex, regulates the expression of several candidate genes for autism spectrum disorders (ASD). Although TBR1 has been reported as a high-confidence risk gene for ASD and intellectual disability (ID) in functional and clinical reports since 2011, TBR1 has only recently been recorded as a human disease gene in the OMIM database. Currently, the neurodevelopmental disorders and structural brain anomalies associated with TBR1 variants are not well characterized. Through international data sharing, we collected data from 25 unreported individuals and compared them with data from the literature. We evaluated structural brain anomalies in seven individuals by analysis of MRI images, and compared these with anomalies observed in TBR1 mutant mice. The phenotype included ID in all individuals, associated to autistic traits in 76% of them. No recognizable facial phenotype could be identified. MRI analysis revealed a reduction of the anterior commissure and suggested new features including dysplastic hippocampus and subtle neocortical dysgenesis. This report supports the role of TBR1 in ID associated with autistic traits and suggests new structural brain malformations in humans. We hope this work will help geneticists to interpret TBR1 variants and diagnose ASD probands

Etude de la syntaxine 8 humaine (caractérisation génomique et relations fonctionnelles avec CFTR)

Le gène codant pour la syntaxine 8 humaine (Syn8), une protéine t-SNARE, a été clonée par un criblage double-hybride en utilisant le domaine R de CFTR comme appât. STX8 est morcelé en 8 exons, sur un minimum de 350 kpb, en 17p12. Nous avons localisé un point d'initiation de la transcription, compatible avec la taille de l'ARNm (1,4 kb). La région promotrice a été clonée puis son activité a été évaluée. Par biochimie, nous avons montré une interaction faible entre Syn8 et CFTR puis confirmé leur présence au sein d'un même complexe. Nous avons observé que la surexpression de Syn8 provoquait une inhibition de l'activité de CFTR, qui n'est plus localisé à la membrane plasmique, mais se est concentré dans les endosomes du recyclage. Nos résultats montrent que Syn8 participe au transport et à la régulation de CFTR. Ces informations permettront de préciser les mécanismes du transport intracellulaire de CFTR qui est perturbé chez la plupart des sujets atteints de mucoviscidose.Syntaxin 8, a new t-SNARE protein, was previously cloned with the two hybrid system using the R domain of CFTR as a bait. The human STX8 gene is composed of 8 exons spanning a 350 kb genomic DNA region on chromosome 17. A transcription start was found concordant with the mRNA size (1.4 kb). The promoter region was cloned and its activity was characterized. Biochemical experiments exhibited a weak interaction between CFTR and syntaxin 8 but confirmed that they belonged to a same complex. Syntaxin 8 overexpression led to a strong inhibition of CFTR activity. Indeed CFTR was not localized on plasma membrane but was accumulated in recycling endosomes. Our results show that syntaxin 8 participates directly to CFTR transport and regulates its chloride channel activity. These data could bring some new clues to precise the different steps of CFTR transport, between the endoplasmic reticulum to the plasma membrane, which is disrupted in most of cystic fibrosis patient.POITIERS-BU Sciences (861942102) / SudocSudocFranceF

Quand le NGS aide à résoudre une énigme diagnostique

L’amyotrophie spinale proximale prédominant aux membres inférieurs (ou SMA-LED pour spinal muscular atrophy with lower extremities predominance) est une forme rare de SMA, le plus souvent secondaire à une mutation du gène DYNC1H1. Ce gène code pour les chaines lourdes du complexe dynéine responsable du transport rétrograde de la synapse vers le corps cellulaire neuronal. Le spectre phénotypique des mutations du gène DYNC1H1 est vaste, mais l’association d’une pathologie neurologique périphérique (SMA-LED ou maladie de Charcot Marie Tooth de type 2) à une atteinte neurologique centrale (déficience cognitive avec ou sans malformation corticale) peut guider le clinicien

Penetrance, variable expressivity and monogenic neurodevelopmental disorders.

PURPOSE Incomplete penetrance is observed for most monogenic diseases. However, for neurodevelopmental disorders, the interpretation of single and multi-nucleotide variants (SNV/MNVs) is usually based on the paradigm of complete penetrance. METHOD From 2020 to 2022, we proposed a collaboration study with the French molecular diagnosis for intellectual disability network. The aim was to recruit families for whom the index case, diagnosed with a neurodevelopmental disorder, was carrying a pathogenic or likely pathogenic variant for an OMIM morbid gene and inherited from an asymptomatic parent. Grandparents were analyzed when available for segregation study. RESULTS We identified 12 patients affected by a monogenic neurodevelopmental disorder caused by likely pathogenic or pathogenic variant (SNV/MNV) inherited from an asymptomatic parent. These genes were usually associated with de novo variants. The patients carried different variants (1 splice-site variant, 4 nonsense and 7 frameshift) in 11 genes: CAMTA1, MBD5, KMT2C, KMT2E, ZMIZ1, MN1, NDUFB11, CUL3, MED13, ARID2 and RERE. Grandparents have been tested in 6 families, and each time the variant was confirmed de novo in the healthy carrier parent. CONCLUSION Incomplete penetrance for SNV and MNV in neurodevelopmental disorders might be more frequent than previously thought. This point is crucial to consider for interpretation of variants, family investigation, genetic counseling, and prenatal diagnosis. Molecular mechanisms underlying this incomplete penetrance still need to be identified

Additional file 1: Table S1. of Copy number variants and rasopathies: germline KRAS duplication in a patient with syndrome including pigmentation abnormalities

Gene content of the ~10.5-Mb chromosome 12p duplication between nt 23,728,536 and nt 34,189,943 (NCBI Build hg19), including 49 protein coding genes, two microRNA genes, and one long non coding RNA gene. (DOCX 24 kb

Influence of the Duplication of CFTR Exon 9 and Its Flanking Sequences on Diagnosis of Cystic Fibrosis Mutations

The DNA sequences of seven regions in the human genome were examined for sequence identity with exon 9 of the cystic fibrosis transmembrane conductance regulator (CFTR) gene, which is mutated in cystic fibrosis, and its intronic boundaries. These sequences were 95% to 96% homologous. Based on this nucleotide sequence similarity, PCR primers for CFTR exon 9 can potentially anneal with other homologous sequences in the human genome. Sequence alignment analysis of the CFTR exon 9 homologous sequences revealed that five registered mutations in the Cystic Fibrosis Mutation Database may be due to the undesired annealing of primers to a homologous sequence, resulting in inappropriate PCR amplification. For this reason, we propose that certain pseudomutations may result from the similarity between CFTR exon 9 (and its flanking introns) and related sequences in the human genome. Here we show that two mutations previously described in the CFTR database (c.1392 + 6insC; c.1392 + 12G>A) were inappropriately attributed to two individuals who sought carrier testing. A more detailed study by either direct sequencing or subcloning and sequencing of PCR products using specially designed primers revealed that these apparent mutations were not, in fact, present in CFTR. In addition, we present new PCR conditions that permit specific amplification of CFTR exon 9 and its flanking regions

CHARGE syndrome: a recurrent hotspot of mutations in CHD7 IVS25 analyzed by bioinformatic tools and minigene assays

CHARGE syndrome is a rare genetic disorder mainly due to de novo and private truncating mutations of CHD7 gene. Here we report an intriguing hot spot of intronic mutations (c.5405-7G > A, c.5405-13G > A, c.5405-17G > A and c.5405-18C > A) located in CHD7 IVS25. Combining computational in silico analysis, experimental branch-point determination and in vitro minigene assays, our study explains this mutation hot spot by a particular genomic context, including the weakness of the IVS25 natural acceptor-site and an unconventional lariat sequence localized outside the common 40 bp upstream the acceptor splice site. For each of the mutations reported here, bioinformatic tools indicated a newly created 3' splice site, of which the existence was confirmed using pSpliceExpress, an easy-to-use and reliable splicing reporter tool. Our study emphasizes the idea that combining these two complementary approaches could increase the efficiency of routine molecular diagnosis