Haploinsufficiency of ARFGEF1 is associated with developmental delay, intellectual disability, and epilepsy with variable expressivity

ADP ribosylation factor guanine nucleotide exchange factors (ARFGEFs) are a family of proteins implicated in cellular trafficking between the Golgi apparatus and the plasma membrane through vesicle formation. Among them is ARFGEF1/BIG1, a protein involved in axon elongation, neurite development, and polarization processes. ARFGEF1 has been previously suggested as a candidate gene for different types of epilepsies, although its implication in human disease has not been well characterized. International data sharing, in silico predictions, and in vitro assays with minigene study, western blot analyses, and RNA sequencing. We identified 13 individuals with heterozygous likely pathogenic variants in ARFGEF1. These individuals displayed congruent clinical features of developmental delay, behavioral problems, abnormal findings on brain magnetic resonance image (MRI), and epilepsy for almost half of them. While nearly half of the cohort carried de novo variants, at least 40% of variants were inherited from mildly affected parents who were clinically re-evaluated by reverse phenotyping. Our in silico predictions and in vitro assays support the contention that ARFGEF1-related conditions are caused by haploinsufficiency, and are transmitted in an autosomal dominant fashion with variable expressivity. We provide evidence that loss-of-function variants in ARFGEF1 are implicated in sporadic and familial cases of developmental delay with or without epilepsy

Heterozygous Variants in KDM4B Lead to Global Developmental Delay and Neuroanatomical Defects

KDM4B is a lysine-specific demethylase with a preferential activity on H3K9 tri/di-methylation (H3K9me3/2)-modified histones. H3K9 tri/di-demethylation is an important epigenetic mechanism responsible for silencing of gene expression in animal development and cancer. However, the role of KDM4B on human development is still poorly characterized. Through international data sharing, we gathered a cohort of nine individuals with mono-allelic de novo or inherited variants in KDM4B. All individuals presented with dysmorphic features and global developmental delay (GDD) with language and motor skills most affected. Three individuals had a history of seizures, and four had anomalies on brain imaging ranging from agenesis of the corpus callosum with hydrocephalus to cystic formations, abnormal hippocampi, and polymicrogyria. In mice, lysine demethylase 4B is expressed during brain development with high levels in the hippocampus, a region important for learning and memory. To understand how KDM4B variants can lead to GDD in humans, we assessed the effect of KDM4B disruption on brain anatomy and behavior through an in vivo heterozygous mouse model (Kdm4b+/-), focusing on neuroanatomical changes. In mutant mice, the total brain volume was significantly reduced with decreased size of the hippocampal dentate gyrus, partial agenesis of the corpus callosum, and ventriculomegaly. This report demonstrates that variants in KDM4B are associated with GDD/ intellectual disability and neuroanatomical defects. Our findings suggest that KDM4B variation leads to a chromatinopathy, broadening the spectrum of this group of Mendelian disorders caused by alterations in epigenetic machinery

Clinical spectrum of MTOR-related hypomelanosis of Ito with neurodevelopmental abnormalities.

PURPOSE: Hypomelanosis of Ito (HI) is a skin marker of somatic mosaicism. Mosaic MTOR pathogenic variants have been reported in HI with brain overgrowth. We sought to delineate further the pigmentary skin phenotype and clinical spectrum of neurodevelopmental manifestations of MTOR-related HI. METHODS: From two cohorts totaling 71 patients with pigmentary mosaicism, we identified 14 patients with Blaschko-linear and one with flag-like pigmentation abnormalities, psychomotor impairment or seizures, and a postzygotic MTOR variant in skin. Patient records, including brain magnetic resonance image (MRI) were reviewed. Immunostaining (n = 3) for melanocyte markers and ultrastructural studies (n = 2) were performed on skin biopsies. RESULTS: MTOR variants were present in skin, but absent from blood in half of cases. In a patient (p.[Glu2419Lys] variant), phosphorylation of p70S6K was constitutively increased. In hypopigmented skin of two patients, we found a decrease in stage 4 melanosomes in melanocytes and keratinocytes. Most patients (80%) had macrocephaly or (hemi)megalencephaly on MRI. CONCLUSION: MTOR-related HI is a recognizable neurocutaneous phenotype of patterned dyspigmentation, epilepsy, intellectual deficiency, and brain overgrowth, and a distinct subtype of hypomelanosis related to somatic mosaicism. Hypopigmentation may be due to a defect in melanogenesis, through mTORC1 activation, similar to hypochromic patches in tuberous sclerosis complex

Missense variants in ANKRD11 cause KBG syndrome by impairment of stability or transcriptional activity of the encoded protein

Purpose Although haploinsufficiency of ANKRD11 is among the most common genetic causes of neurodevelopmental disorders, the role of rare ANKRD11 missense variation remains unclear. We characterized clinical, molecular, and functional spectra of ANKRD11 missense variants. Methods We collected clinical information of individuals with ANKRD11 missense variants and evaluated phenotypic fit to KBG syndrome. We assessed pathogenicity of variants through in silico analyses and cell-based experiments. Results We identified 20 unique, mostly de novo, ANKRD11 missense variants in 29 individuals, presenting with syndromic neurodevelopmental disorders similar to KBG syndrome caused by ANKRD11 protein truncating variants or 16q24.3 microdeletions. Missense variants significantly clustered in repression domain 2 at the ANKRD11 C-terminus. Of the 10 functionally studied missense variants, 6 reduced ANKRD11 stability. One variant caused decreased proteasome degradation and loss of ANKRD11 transcriptional activity. Conclusion Our study indicates that pathogenic heterozygous ANKRD11 missense variants cause the clinically recognizable KBG syndrome. Disrupted transrepression capacity and reduced protein stability each independently lead to ANKRD11 loss-of-function, consistent with haploinsufficiency. This highlights the diagnostic relevance of ANKRD11 missense variants, but also poses diagnostic challenges because the KBG-associated phenotype may be mild and inherited pathogenic ANKRD11 (missense) variants are increasingly observed, warranting stringent variant classification and careful phenotyping

A Solve-RD ClinVar-based reanalysis of 1522 index cases from ERN-ITHACA reveals common pitfalls and misinterpretations in exome sequencing

Purpose Within the Solve-RD project (https://solve-rd.eu/), the European Reference Network for Intellectual disability, TeleHealth, Autism and Congenital Anomalies aimed to investigate whether a reanalysis of exomes from unsolved cases based on ClinVar annotations could establish additional diagnoses. We present the results of the “ClinVar low-hanging fruit” reanalysis, reasons for the failure of previous analyses, and lessons learned. Methods Data from the first 3576 exomes (1522 probands and 2054 relatives) collected from European Reference Network for Intellectual disability, TeleHealth, Autism and Congenital Anomalies was reanalyzed by the Solve-RD consortium by evaluating for the presence of single-nucleotide variant, and small insertions and deletions already reported as (likely) pathogenic in ClinVar. Variants were filtered according to frequency, genotype, and mode of inheritance and reinterpreted. Results We identified causal variants in 59 cases (3.9%), 50 of them also raised by other approaches and 9 leading to new diagnoses, highlighting interpretation challenges: variants in genes not known to be involved in human disease at the time of the first analysis, misleading genotypes, or variants undetected by local pipelines (variants in off-target regions, low quality filters, low allelic balance, or high frequency). Conclusion The “ClinVar low-hanging fruit” analysis represents an effective, fast, and easy approach to recover causal variants from exome sequencing data, herewith contributing to the reduction of the diagnostic deadlock

Cutaneous mosaic syndromes associated with early postzygotic activating BRAF mutations

IF 3.528International audienc

Mutation en mosaïque de KITLG dans l’hypermélanose nævoïde

International audienceIntroductionL’hypermélanose nævoïde linéaire et en volutes est une pigmentation maculeuse considérée comme une manifestation non spécifique de mosaïcisme génétique. Elle a parfois été confondue avec la phase pigmentaire de l’incontinentia pigmenti, plus transitoire. Elle peut être associée à des anomalies chromosomiques de la région centromérique du chromosome X (Xp), en mosaïque ou non, mais sa cause est restée jusqu’ici inconnue. Nous rapportons ici pour la première fois une anomalie monogénique en mosaïque à l’origine de ce trouble pigmentaire.ObservationsNous avons effectué un séquençage d’exome complet en profondeur (200X) sur ADN de biopsie cutanée en peau pigmentée et ADN sanguin chez un patient de 6 ans précédemment rapporté présentant une hyperpigmentation congénitale linéaire sur le tronc et les membres, suivant les lignes de Blaschko, non évolutive. L’histologie montrait une hypermélaninose épidermique basale et supra-basale sans incontinence pigmentaire. Il n’y avait pas d’anomalie mélanocytaire. Aucune autre atteinte cutanée ou extra-cutanée, en particulier neurologique, n’était notée.RésultatsUne mutation hétérozygote postzygotique dans l’exon 4 de KITLG c.329A > G (p.Asp110Gly) a été identifiée sur la peau. Elle a été confirmée par séquençage ciblé en profondeur, touchant 28 % des allèles sur la peau et 18 % des allèles dans le sang. L’immunohistochimie a montré une augmentation de l’expression de KITLG sur des kératinocytes en peau pigmentée.DiscussionLe ligand de c-KIT (KITLG) aussi connu sous le nom de stem cell factor (SCF) est une protéine qui régule la pigmentation cutanée par la voie ras/MAPK. Il contrôle la migration, la prolifération et la survie mélanocytaires et la synthèse de la mélanine. Son rôle dans des anomalies héréditaires de la pigmentation cutanée a déjà été mis en évidence puisque des mutations germinales de KITLG ont été rapportées dans l’hyper-hypopigmentation familiale progressive (FPHH, OMIM 145250). Dans cette affection héréditaire, les macules pigmentées surviennent précocement et augmentent par la suite en nombre et en taille, s’associant à des macules hypopigmentées. D’autres mutations de KITLG ont aussi été identifiées dans des formes isolées de surdité et de syndrome de Waardenburg de type 2 avec hypochromie. Malgré l’absence d’analyse fonctionnelle, nous avons retrouvé une surexpression épidermique de KITLG, ce qui suggère que p.Asp110Gly est une mutation activatrice (gain-de-fonction).ConclusionChez ce patient, l’hypermélanose nævoïde constitue une forme en mosaïque de l’hyper-hypopigmentation familiale progressive par mutation de KITLG

Reverse Phenotyping in Patients with Skin Capillary Malformations and Mosaic GNAQ or GNA11 Mutations Defines a Clinical Spectrum with Genotype-Phenotype Correlation

International audienceNo abstract availabl

Author Correction: Postzygotic inactivating mutations of RHOA cause a mosaic neuroectodermal syndrome [Correction to: Nature Genetics https://doi.org/10.1038/s41588-019-0498-4, published online 30 September 2019]

Indexation en cours. In the version of this article initially published, support from the Wellcome Trust and NIHR to author Veronica A. Kinsler was not included in the Acknowledgements. The error has been corrected in the HTML and PDF versions of the article.International audienceAn amendment to this paper has been published and can be accessed via a link at the top of the paper