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1.
Cell ; 157(3): 651-63, 2014 Apr 24.
Article in English | MEDLINE | ID: mdl-24766810

ABSTRACT

Neurodegenerative diseases can occur so early as to affect neurodevelopment. From a cohort of more than 2,000 consanguineous families with childhood neurological disease, we identified a founder mutation in four independent pedigrees in cleavage and polyadenylation factor I subunit 1 (CLP1). CLP1 is a multifunctional kinase implicated in tRNA, mRNA, and siRNA maturation. Kinase activity of the CLP1 mutant protein was defective, and the tRNA endonuclease complex (TSEN) was destabilized, resulting in impaired pre-tRNA cleavage. Germline clp1 null zebrafish showed cerebellar neurodegeneration that was rescued by wild-type, but not mutant, human CLP1 expression. Patient-derived induced neurons displayed both depletion of mature tRNAs and accumulation of unspliced pre-tRNAs. Transfection of partially processed tRNA fragments into patient cells exacerbated an oxidative stress-induced reduction in cell survival. Our data link tRNA maturation to neuronal development and neurodegeneration through defective CLP1 function in humans.


Subject(s)
Cerebellum/growth & development , Cerebellum/pathology , Cleavage And Polyadenylation Specificity Factor/metabolism , Nuclear Proteins/genetics , Phosphotransferases/genetics , RNA Splicing , RNA, Transfer/genetics , Transcription Factors/genetics , Zebrafish Proteins/metabolism , Animals , Brain/metabolism , Brain/pathology , Cleavage And Polyadenylation Specificity Factor/genetics , Female , Humans , Male , Mice , Models, Molecular , Neurodegenerative Diseases/genetics , Neurodegenerative Diseases/pathology , Nuclear Proteins/metabolism , Pedigree , Phosphotransferases/metabolism , RNA, Transfer/metabolism , Saccharomyces cerevisiae/metabolism , Transcription Factors/metabolism , Zebrafish , Zebrafish Proteins/genetics
2.
Mol Cell ; 81(22): 4663-4676.e8, 2021 11 18.
Article in English | MEDLINE | ID: mdl-34637754

ABSTRACT

The heterogeneous family of complexes comprising Polycomb repressive complex 1 (PRC1) is instrumental for establishing facultative heterochromatin that is repressive to transcription. However, two PRC1 species, ncPRC1.3 and ncPRC1.5, are known to comprise novel components, AUTS2, P300, and CK2, that convert this repressive function to that of transcription activation. Here, we report that individuals harboring mutations in the HX repeat domain of AUTS2 exhibit defects in AUTS2 and P300 interaction as well as a developmental disorder reflective of Rubinstein-Taybi syndrome, which is mainly associated with a heterozygous pathogenic variant in CREBBP/EP300. Moreover, the absence of AUTS2 or mutation in its HX repeat domain gives rise to misregulation of a subset of developmental genes and curtails motor neuron differentiation of mouse embryonic stem cells. The transcription factor nuclear respiratory factor 1 (NRF1) has a novel and integral role in this neurodevelopmental process, being required for ncPRC1.3 recruitment to chromatin.


Subject(s)
Brain/metabolism , CREB-Binding Protein/genetics , Cytoskeletal Proteins/metabolism , E1A-Associated p300 Protein/genetics , Embryonic Stem Cells/metabolism , Nuclear Respiratory Factor 1/metabolism , Transcription Factors/metabolism , Animals , Cell Differentiation , Chromatin/chemistry , Female , Genomics , HEK293 Cells , Heterozygote , Humans , Male , Mice , Neurons/metabolism , Protein Binding , Protein Domains , Proteomics , Transcriptional Activation
3.
Am J Hum Genet ; 111(7): 1330-1351, 2024 07 11.
Article in English | MEDLINE | ID: mdl-38815585

ABSTRACT

Epigenetic dysregulation has emerged as an important etiological mechanism of neurodevelopmental disorders (NDDs). Pathogenic variation in epigenetic regulators can impair deposition of histone post-translational modifications leading to aberrant spatiotemporal gene expression during neurodevelopment. The male-specific lethal (MSL) complex is a prominent multi-subunit epigenetic regulator of gene expression and is responsible for histone 4 lysine 16 acetylation (H4K16ac). Using exome sequencing, here we identify a cohort of 25 individuals with heterozygous de novo variants in MSL complex member MSL2. MSL2 variants were associated with NDD phenotypes including global developmental delay, intellectual disability, hypotonia, and motor issues such as coordination problems, feeding difficulties, and gait disturbance. Dysmorphisms and behavioral and/or psychiatric conditions, including autism spectrum disorder, and to a lesser extent, seizures, connective tissue disease signs, sleep disturbance, vision problems, and other organ anomalies, were observed in affected individuals. As a molecular biomarker, a sensitive and specific DNA methylation episignature has been established. Induced pluripotent stem cells (iPSCs) derived from three members of our cohort exhibited reduced MSL2 levels. Remarkably, while NDD-associated variants in two other members of the MSL complex (MOF and MSL3) result in reduced H4K16ac, global H4K16ac levels are unchanged in iPSCs with MSL2 variants. Regardless, MSL2 variants altered the expression of MSL2 targets in iPSCs and upon their differentiation to early germ layers. Our study defines an MSL2-related disorder as an NDD with distinguishable clinical features, a specific blood DNA episignature, and a distinct, MSL2-specific molecular etiology compared to other MSL complex-related disorders.


Subject(s)
Epilepsy , Neurodevelopmental Disorders , Ubiquitin-Protein Ligases , Adolescent , Child , Child, Preschool , Female , Humans , Male , Developmental Disabilities/genetics , DNA Methylation/genetics , Epigenesis, Genetic , Epilepsy/genetics , Histones/metabolism , Histones/genetics , Induced Pluripotent Stem Cells/metabolism , Intellectual Disability/genetics , Neurodevelopmental Disorders/genetics , Phenotype , Ubiquitin-Protein Ligases/metabolism
4.
Hum Mol Genet ; 31(3): 440-454, 2022 02 03.
Article in English | MEDLINE | ID: mdl-34505148

ABSTRACT

Recently, others and we identified de novo FBXO11 (F-Box only protein 11) variants as causative for a variable neurodevelopmental disorder (NDD). We now assembled clinical and mutational information on 23 additional individuals. The phenotypic spectrum remains highly variable, with developmental delay and/or intellectual disability as the core feature and behavioral anomalies, hypotonia and various facial dysmorphism as frequent aspects. The mutational spectrum includes intragenic deletions, likely gene disrupting and missense variants distributed across the protein. To further characterize the functional consequences of FBXO11 missense variants, we analyzed their effects on protein expression and localization by overexpression of 17 different mutant constructs in HEK293 and HeLa cells. We found that the majority of missense variants resulted in subcellular mislocalization and/or reduced FBXO11 protein expression levels. For instance, variants located in the nuclear localization signal and the N-terminal F-Box domain lead to altered subcellular localization with exclusion from the nucleus or the formation of cytoplasmic aggregates and to reduced protein levels in western blot. In contrast, variants localized in the C-terminal Zn-finger UBR domain lead to an accumulation in the cytoplasm without alteration of protein levels. Together with the mutational data, our functional results suggest that most missense variants likely lead to a loss of the original FBXO11 function and thereby highlight haploinsufficiency as the most likely disease mechanism for FBXO11-associated NDDs.


Subject(s)
F-Box Proteins , Intellectual Disability , Neurodevelopmental Disorders , F-Box Proteins/genetics , HEK293 Cells , HeLa Cells , Humans , Intellectual Disability/genetics , Mutation, Missense/genetics , Neurodevelopmental Disorders/genetics , Protein-Arginine N-Methyltransferases/genetics
5.
Am J Med Genet A ; 194(7): e63559, 2024 07.
Article in English | MEDLINE | ID: mdl-38421105

ABSTRACT

The disconnected (disco)-interacting protein 2 (DIP2) gene was first identified in D. melanogaster and contains a DNA methyltransferase-associated protein 1 (DMAP1) binding domain, Acyl-CoA synthetase domain and AMP-binding sites. DIP2 regulates axonal bifurcation of the mushroom body neurons in D. melanogaster and is required for axonal regeneration in the neurons of C. elegans. The DIP2 homologues in vertebrates, Disco-interacting protein 2 homolog A (DIP2A), Disco-interacting protein 2 homolog B (DIP2B), and Disco-interacting protein 2 homolog C (DIP2C), are highly conserved and expressed widely in the central nervous system. Although there is evidence that DIP2C plays a role in cognition, reports of pathogenic variants in these genes are rare and their significance is uncertain. We present 23 individuals with heterozygous DIP2C variants, all manifesting developmental delays that primarily affect expressive language and speech articulation. Eight patients had de novo variants predicting loss-of-function in the DIP2C gene, two patients had de novo missense variants, three had paternally inherited loss of function variants and six had maternally inherited loss-of-function variants, while inheritance was unknown for four variants. Four patients had cardiac defects (hypertrophic cardiomyopathy, atrial septal defects, and bicuspid aortic valve). Minor facial anomalies were inconsistent but included a high anterior hairline with a long forehead, broad nasal tip, and ear anomalies. Brainspan analysis showed elevated DIP2C expression in the human neocortex at 10-24 weeks after conception. With the cases presented herein, we provide phenotypic and genotypic data supporting the association between loss-of-function variants in DIP2C with a neurocognitive phenotype.


Subject(s)
Haploinsufficiency , Language Development Disorders , Humans , Male , Female , Haploinsufficiency/genetics , Language Development Disorders/genetics , Language Development Disorders/pathology , Language Development Disorders/physiopathology , Child, Preschool , Child , Infant , Phenotype , Genetic Predisposition to Disease
7.
J Med Genet ; 60(6): 597-607, 2023 06.
Article in English | MEDLINE | ID: mdl-36328423

ABSTRACT

BACKGROUND: Heterozygous disruptions of FOXP2 were the first identified molecular cause for severe speech disorder: childhood apraxia of speech (CAS), and yet few cases have been reported, limiting knowledge of the condition. METHODS: Here we phenotyped 28 individuals from 17 families with pathogenic FOXP2-only variants (12 loss-of-function, five missense variants; 14 males; aged 2 to 62 years). Health and development (cognitive, motor, social domains) were examined, including speech and language outcomes with the first cross-linguistic analysis of English and German. RESULTS: Speech disorders were prevalent (23/25, 92%) and CAS was most common (22/25, 88%), with similar speech presentations across English and German. Speech was still impaired in adulthood, and some speech sounds (eg, 'th', 'r', 'ch', 'j') were never acquired. Language impairments (21/25, 84%) ranged from mild to severe. Comorbidities included feeding difficulties in infancy (10/26, 38%), fine (13/26, 50%) and gross (13/26, 50%) motor impairment, anxiety (5/27, 19%), depression (6/27, 22%) and sleep disturbance (10/24, 42%). Physical features were common (22/27, 81%) but with no consistent pattern. Cognition ranged from average to mildly impaired and was incongruent with language ability; for example, seven participants with severe language disorder had average non-verbal cognition. CONCLUSIONS: Although we identify an increased prevalence of conditions like anxiety, depression and sleep disturbance, we confirm that the consequences of FOXP2 dysfunction remain relatively specific to speech disorder, as compared with other recently identified monogenic conditions associated with CAS. Thus, our findings reinforce that FOXP2 provides a valuable entry point for examining the neurobiological bases of speech disorder.


Subject(s)
Apraxias , Language Disorders , Male , Humans , Child , Speech Disorders/genetics , Language Disorders/epidemiology , Language Disorders/genetics , Speech , Apraxias/genetics , Mutation, Missense/genetics , Forkhead Transcription Factors/genetics
8.
Pediatr Hematol Oncol ; 41(7): 530-539, 2024 Oct.
Article in English | MEDLINE | ID: mdl-38840569

ABSTRACT

Clonal hematopoiesis of indeterminate potential (CHIP) describes recurrent somatic gene mutations in the blood of healthy individuals, associated with higher risk for hematological malignancies and higher all-cause mortality by cardiovascular disease. CHIP increases with age and is more common in adult patients after chemotherapy or radiation for cancer. Furthermore, in some adult patients undergoing autologous stem cell transplantation (ASCT) or thereafter, CHIP has been identified. In children and adolescents, it remains unclear how cellular stressors such as cytotoxic therapy influence the incidence and expansion of CHIP. We conducted a retrospective study on 33 pediatric patients mostly with solid tumors undergoing ASCT for presence of CHIP. We analyzed CD34+ selected peripheral blood stem cell grafts after several cycles of chemotherapy, prior to cell infusion, by next-generation sequencing including 18 "CHIP-genes". Apart from a somatic variant in TP53 in one patient no other variants indicative of CHIP were identified. As a CHIP-unrelated finding, germline variants in CHEK2 and in ATM were identified in two and four patients, respectively. In conclusion, we could not detect "typical" CHIP variants in our cohort of pediatric cancer patients undergoing ASCT. However, more studies with larger patient numbers are necessary to assess if chemotherapy in the pediatric setting contributes to an increased CHIP incidence and at what time point.


Subject(s)
Clonal Hematopoiesis , Transplantation, Autologous , Humans , Male , Child , Female , Adolescent , Retrospective Studies , Child, Preschool , Infant , Checkpoint Kinase 2/genetics , Hematopoietic Stem Cell Transplantation , Ataxia Telangiectasia Mutated Proteins/genetics , Mutation , Neoplasms/therapy , Neoplasms/genetics
9.
Am J Hum Genet ; 107(3): 544-554, 2020 09 03.
Article in English | MEDLINE | ID: mdl-32730804

ABSTRACT

RNA polymerase II interacts with various other complexes and factors to ensure correct initiation, elongation, and termination of mRNA transcription. One of these proteins is SR-related CTD-associated factor 4 (SCAF4), which is important for correct usage of polyA sites for mRNA termination. Using exome sequencing and international matchmaking, we identified nine likely pathogenic germline variants in SCAF4 including two splice-site and seven truncating variants, all residing in the N-terminal two thirds of the protein. Eight of these variants occurred de novo, and one was inherited. Affected individuals demonstrated a variable neurodevelopmental disorder characterized by mild intellectual disability, seizures, behavioral abnormalities, and various skeletal and structural anomalies. Paired-end RNA sequencing on blood lymphocytes of SCAF4-deficient individuals revealed a broad deregulation of more than 9,000 genes and significant differential splicing of more than 2,900 genes, indicating an important role of SCAF4 in mRNA processing. Knockdown of the SCAF4 ortholog CG4266 in the model organism Drosophila melanogaster resulted in impaired locomotor function, learning, and short-term memory. Furthermore, we observed an increased number of active zones in larval neuromuscular junctions, representing large glutamatergic synapses. These observations indicate a role of CG4266 in nervous system development and function and support the implication of SCAF4 in neurodevelopmental phenotypes. In summary, our data show that heterozygous, likely gene-disrupting variants in SCAF4 are causative for a variable neurodevelopmental disorder associated with impaired mRNA processing.


Subject(s)
Intellectual Disability/genetics , Neurodevelopmental Disorders/genetics , Seizures/genetics , Serine-Arginine Splicing Factors/genetics , Animals , Child , Drosophila melanogaster/genetics , Female , Gene Knockdown Techniques , Genetic Variation/genetics , Heterozygote , Humans , Intellectual Disability/physiopathology , Locomotion/genetics , Male , Mutation/genetics , Neurodevelopmental Disorders/physiopathology , RNA Polymerase II/genetics , RNA Processing, Post-Transcriptional/genetics , RNA, Messenger/genetics , Seizures/physiopathology , Exome Sequencing
10.
Genet Med ; 25(7): 100839, 2023 Jul.
Article in English | MEDLINE | ID: mdl-37057675

ABSTRACT

PURPOSE: LHX2 encodes the LIM homeobox 2 transcription factor (LHX2), which is highly expressed in brain and well conserved across species, but it has not been clearly linked to neurodevelopmental disorders (NDDs) to date. METHODS: Through international collaboration, we identified 19 individuals from 18 families with variable neurodevelopmental phenotypes, carrying a small chromosomal deletion, likely gene-disrupting or missense variants in LHX2. Functional consequences of missense variants were investigated in cellular systems. RESULTS: Affected individuals presented with developmental and/or behavioral abnormalities, autism spectrum disorder, variable intellectual disability, and microcephaly. We observed nucleolar accumulation for 2 missense variants located within the DNA-binding HOX domain, impaired interaction with co-factor LDB1 for another variant located in the protein-protein interaction-mediating LIM domain, and impaired transcriptional activation by luciferase assay for 4 missense variants. CONCLUSION: We implicate LHX2 haploinsufficiency by deletion and likely gene-disrupting variants as causative for a variable NDD. Our findings suggest a loss-of-function mechanism also for likely pathogenic LHX2 missense variants. Together, our observations underscore the importance of LHX2 in the nervous system and for variable neurodevelopmental phenotypes.


Subject(s)
Autism Spectrum Disorder , Intellectual Disability , Neurodevelopmental Disorders , Humans , LIM-Homeodomain Proteins/genetics , Autism Spectrum Disorder/genetics , Haploinsufficiency/genetics , Neurodevelopmental Disorders/pathology , Transcription Factors/genetics , Intellectual Disability/genetics , Intellectual Disability/complications
11.
Cell ; 135(1): 37-48, 2008 Oct 03.
Article in English | MEDLINE | ID: mdl-18854153

ABSTRACT

Plasmacytoid dendritic cells (PDCs) represent a unique immune cell type specialized in type I interferon (IFN) secretion in response to viral nucleic acids. The molecular control of PDC lineage specification has been poorly understood. We report that basic helix-loop-helix transcription factor (E protein) E2-2/Tcf4 is preferentially expressed in murine and human PDCs. Constitutive or inducible deletion of murine E2-2 blocked the development of PDCs but not of other lineages and abolished IFN response to unmethylated DNA. Moreover, E2-2 haploinsufficiency in mice and in human Pitt-Hopkins syndrome patients was associated with aberrant expression profile and impaired IFN response of the PDC. E2-2 directly activated multiple PDC-enriched genes, including transcription factors involved in PDC development (SpiB, Irf8) and function (Irf7). These results identify E2-2 as a specific transcriptional regulator of the PDC lineage in mice and humans and reveal a key function of E proteins in the innate immune system.


Subject(s)
Dendritic Cells/immunology , Nerve Tissue Proteins/immunology , TCF Transcription Factors/immunology , Adolescent , Animals , Basic Helix-Loop-Helix Leucine Zipper Transcription Factors , Child , Child, Preschool , DNA-Binding Proteins , Dendritic Cells/metabolism , Humans , Hyperventilation/immunology , Immunity, Innate , Intellectual Disability/immunology , Interferons/immunology , Mice , Syndrome , Transcription Factor 4 , Transcription Factor 7-Like 2 Protein , Transcription Factors
12.
J Med Genet ; 59(10): 965-975, 2022 Oct.
Article in English | MEDLINE | ID: mdl-34930816

ABSTRACT

BACKGROUND: High-impact pathogenic variants in more than a thousand genes are involved in Mendelian forms of neurodevelopmental disorders (NDD). METHODS: This study describes the molecular and clinical characterisation of 28 probands with NDD harbouring heterozygous AGO1 coding variants, occurring de novo for all those whose transmission could have been verified (26/28). RESULTS: A total of 15 unique variants leading to amino acid changes or deletions were identified: 12 missense variants, two in-frame deletions of one codon, and one canonical splice variant leading to a deletion of two amino acid residues. Recurrently identified variants were present in several unrelated individuals: p.(Phe180del), p.(Leu190Pro), p.(Leu190Arg), p.(Gly199Ser), p.(Val254Ile) and p.(Glu376del). AGO1 encodes the Argonaute 1 protein, which functions in gene-silencing pathways mediated by small non-coding RNAs. Three-dimensional protein structure predictions suggest that these variants might alter the flexibility of the AGO1 linker domains, which likely would impair its function in mRNA processing. Affected individuals present with intellectual disability of varying severity, as well as speech and motor delay, autistic behaviour and additional behavioural manifestations. CONCLUSION: Our study establishes that de novo coding variants in AGO1 are involved in a novel monogenic form of NDD, highly similar to the recently reported AGO2-related NDD.


Subject(s)
Argonaute Proteins , Intellectual Disability , Neurodevelopmental Disorders , Humans , Amino Acids/genetics , Heterozygote , Intellectual Disability/genetics , Intellectual Disability/pathology , Neurodevelopmental Disorders/genetics , Neurodevelopmental Disorders/pathology , RNA, Messenger , Argonaute Proteins/genetics
13.
Genet Med ; 24(6): 1261-1273, 2022 06.
Article in English | MEDLINE | ID: mdl-35341651

ABSTRACT

PURPOSE: This study aimed to undertake a multidisciplinary characterization of the phenotype associated with SOX11 variants. METHODS: Individuals with protein altering variants in SOX11 were identified through exome and genome sequencing and international data sharing. Deep clinical phenotyping was undertaken by referring clinicians. Blood DNA methylation was assessed using Infinium MethylationEPIC array. The expression pattern of SOX11 in developing human brain was defined using RNAscope. RESULTS: We reported 38 new patients with SOX11 variants. Idiopathic hypogonadotropic hypogonadism was confirmed as a feature of SOX11 syndrome. A distinctive pattern of blood DNA methylation was identified in SOX11 syndrome, separating SOX11 syndrome from other BAFopathies. CONCLUSION: SOX11 syndrome is a distinct clinical entity with characteristic clinical features and episignature differentiating it from BAFopathies.


Subject(s)
DNA Methylation , Hypogonadism , Klinefelter Syndrome , Neurodevelopmental Disorders , SOXC Transcription Factors , DNA Methylation/genetics , Humans , Hypogonadism/genetics , Klinefelter Syndrome/genetics , Neurodevelopmental Disorders/genetics , Phenotype , SOXC Transcription Factors/genetics , Exome Sequencing
14.
Clin Genet ; 102(6): 517-523, 2022 12.
Article in English | MEDLINE | ID: mdl-35908153

ABSTRACT

TCF4 haploinsufficiency by deletions, truncating variants or loss-of-function missense variants within the DNA-binding and protein interacting bHLH domain causes Pitt-Hopkins syndrome (PTHS). This neurodevelopmental disorder (NDD) is characterized by severe intellectual disability (ID), epilepsy, hyperbreathing and a typical facial gestalt. Only few aberrations of the N-terminus of TCF4 were associated with milder or atypical phenotypes. By personal communication and searching databases we assembled six cases with the novel, recurrent, de novo missense variant c.1165C > T, p.(Arg389Cys) in TCF4. This variant was identified by diagnostic exome or panel sequencing and is located upstream of the bHLH domain. All six individuals presented with moderate to severe ID with language impairment. Microcephaly occurred in two individuals, epilepsy only in one, and no breathing anomalies or myopia were reported. Facial gestalt showed some aspects of PTHS but was rather non-specific in most individuals. Interestingly, the variant is located within the AD2 activation domain next to a highly conserved coactivator-recruitment motif and might alter interaction with coactivator proteins independently from the bHLH domain. Our findings of a recurrent missense variant outside the bHLH domain in six individuals with an ID phenotype overlapping with but not typical for PTHS delineate a novel genotype-phenotype correlation for TCF4-related NDDs.


Subject(s)
Epilepsy , Intellectual Disability , Humans , Intellectual Disability/genetics , Transcription Factor 4/genetics , Facies , Hyperventilation/diagnosis
15.
Clin Genet ; 102(3): 182-190, 2022 09.
Article in English | MEDLINE | ID: mdl-35662002

ABSTRACT

While inherited hemizygous variants in PHF6 cause X-linked recessive Borjeson-Forssman-Lehmann syndrome (BFLS) in males, de novo heterozygous variants in females are associated with an overlapping but distinct phenotype, including moderate to severe intellectual disability, characteristic facial dysmorphism, dental, finger and toe anomalies, and linear skin pigmentation. By personal communication with colleagues, we assembled 11 additional females with BFLS due to variants in PHF6. We confirm the distinct phenotype to include variable intellectual disability, recognizable facial dysmorphism and other anomalies. We observed skewed X-inactivation in blood and streaky skin pigmentation compatible with functional mosaicism. Variants occurred de novo in 10 individuals, of whom one was only mildly affected and transmitted it to her more severely affected daughter. The mutational spectrum comprises a two-exon deletion, five truncating, one splice-site and three missense variants, the latter all located in the PHD2 domain and predicted to severely destabilize the domain structure. This observation supports the hypothesis of more severe variants in females contributing to gender-specific phenotypes in addition to or in combination with effects of X-inactivation and functional mosaicism. Therefore, our findings further delineate the clinical and mutational spectrum of female BFLS and provide further insights into possible genotype-phenotype correlations between females and males.


Subject(s)
Hypogonadism , Intellectual Disability , Mental Retardation, X-Linked , Musculoskeletal Abnormalities , Repressor Proteins , Epilepsy , Face/abnormalities , Female , Fingers/abnormalities , Growth Disorders , Humans , Hypogonadism/genetics , Intellectual Disability/complications , Male , Mental Retardation, X-Linked/genetics , Musculoskeletal Abnormalities/complications , Obesity , Repressor Proteins/genetics
16.
Am J Med Genet A ; 188(1): 292-297, 2022 01.
Article in English | MEDLINE | ID: mdl-34533271

ABSTRACT

Cohen-Gibson syndrome is a rare genetic disorder, characterized by fetal or early childhood overgrowth and mild to severe intellectual disability. It is caused by heterozygous aberrations in EED, which encodes an evolutionary conserved polycomb group (PcG) protein that forms the polycomb repressive complex-2 (PRC2) together with EZH2, SUZ12, and RBBP7/4. In total, 11 affected individuals with heterozygous pathogenic variants in EED were reported, so far. All variants affect a few key residues within the EED WD40 repeat domain. By trio exome sequencing, we identified the heterozygous missense variant c.581A > G, p.(Asn194Ser) in exon 6 of the EED-gene in an individual with moderate intellectual disability, overgrowth, and epilepsy. The same pathogenic variant was detected in 2 of the 11 previously reported cases. Epilepsy, however, was only diagnosed in one other individual with Cohen-Gibson syndrome before. Our findings further confirm that the WD40 repeat domain represents a mutational hotspot; they also expand the clinical spectrum of Cohen-Gibson syndrome and highlight the clinical variability even in individuals with the same pathogenic variant. Furthermore, they indicate a possible association between Cohen-Gibson syndrome and epilepsy.


Subject(s)
Epilepsy , Intellectual Disability , Child, Preschool , Epilepsy/genetics , Humans , Intellectual Disability/diagnosis , Intellectual Disability/genetics , Mutation , Polycomb Repressive Complex 2/genetics , Exome Sequencing
17.
Am J Hum Genet ; 102(1): 44-57, 2018 01 04.
Article in English | MEDLINE | ID: mdl-29276004

ABSTRACT

Although the role of typical Rho GTPases and other Rho-linked proteins in synaptic plasticity and cognitive function and dysfunction is widely acknowledged, the role of atypical Rho GTPases (such as RHOBTB2) in neurodevelopment has barely been characterized. We have now identified de novo missense variants clustering in the BTB-domain-encoding region of RHOBTB2 in ten individuals with a similar phenotype, including early-onset epilepsy, severe intellectual disability, postnatal microcephaly, and movement disorders. Three of the variants were recurrent. Upon transfection of HEK293 cells, we found that mutant RHOBTB2 was more abundant than the wild-type, most likely because of impaired degradation in the proteasome. Similarly, elevated amounts of the Drosophila ortholog RhoBTB in vivo were associated with seizure susceptibility and severe locomotor defects. Knockdown of RhoBTB in the Drosophila dendritic arborization neurons resulted in a decreased number of dendrites, thus suggesting a role of RhoBTB in dendritic development. We have established missense variants in the BTB-domain-encoding region of RHOBTB2 as causative for a developmental and epileptic encephalopathy and have elucidated the role of atypical Rho GTPase RhoBTB in Drosophila neurological function and possibly dendrite development.


Subject(s)
Drosophila Proteins/genetics , Drosophila melanogaster/genetics , Epilepsy/genetics , GTP-Binding Proteins/genetics , Mutation, Missense/genetics , Tumor Suppressor Proteins/genetics , Adolescent , Amino Acid Sequence , Animals , Behavior, Animal , Child , Child, Preschool , Dendrites/metabolism , Female , GTP-Binding Proteins/chemistry , Gene Dosage , HEK293 Cells , Humans , Male , Phenotype , Synapses/pathology , Tumor Suppressor Proteins/chemistry
18.
Am J Hum Genet ; 103(2): 305-316, 2018 08 02.
Article in English | MEDLINE | ID: mdl-30057029

ABSTRACT

Next-generation sequencing combined with international data sharing has enormously facilitated identification of new disease-associated genes and mutations. This is particularly true for genetically extremely heterogeneous entities such as neurodevelopmental disorders (NDDs). Through exome sequencing and world-wide collaborations, we identified and assembled 20 individuals with de novo variants in FBXO11. They present with mild to severe developmental delay associated with a range of features including short (4/20) or tall (2/20) stature, obesity (5/20), microcephaly (4/19) or macrocephaly (2/19), behavioral problems (17/20), seizures (5/20), cleft lip or palate or bifid uvula (3/20), and minor skeletal anomalies. FBXO11 encodes a member of the F-Box protein family, constituting a subunit of an E3-ubiquitin ligase complex. This complex is involved in ubiquitination and proteasomal degradation and thus in controlling critical biological processes by regulating protein turnover. The identified de novo aberrations comprise two large deletions, ten likely gene disrupting variants, and eight missense variants distributed throughout FBXO11. Structural modeling for missense variants located in the CASH or the Zinc-finger UBR domains suggests destabilization of the protein. This, in combination with the observed spectrum and localization of identified variants and the lack of apparent genotype-phenotype correlations, is compatible with loss of function or haploinsufficiency as an underlying mechanism. We implicate de novo missense and likely gene disrupting variants in FBXO11 in a neurodevelopmental disorder with variable intellectual disability and various other features.


Subject(s)
F-Box Proteins/genetics , Genetic Variation/genetics , Neurodevelopmental Disorders/genetics , Protein-Arginine N-Methyltransferases/genetics , Child , Exome/genetics , Female , Genetic Association Studies/methods , Humans , Intellectual Disability/genetics , Male , Microcephaly/genetics , Proteasome Endopeptidase Complex/genetics , Ubiquitin-Protein Ligases/genetics , Ubiquitination/genetics , Exome Sequencing/methods
19.
Genet Med ; 23(7): 1234-1245, 2021 07.
Article in English | MEDLINE | ID: mdl-33824499

ABSTRACT

PURPOSE: Proline Rich 12 (PRR12) is a gene of unknown function with suspected DNA-binding activity, expressed in developing mice and human brains. Predicted loss-of-function variants in this gene are extremely rare, indicating high intolerance of haploinsufficiency. METHODS: Three individuals with intellectual disability and iris anomalies and truncating de novo PRR12 variants were described previously. We add 21 individuals with similar PRR12 variants identified via matchmaking platforms, bringing the total number to 24. RESULTS: We observed 12 frameshift, 6 nonsense, 1 splice-site, and 2 missense variants and one patient with a gross deletion involving PRR12. Three individuals had additional genetic findings, possibly confounding the phenotype. All patients had developmental impairment. Variable structural eye defects were observed in 12/24 individuals (50%) including anophthalmia, microphthalmia, colobomas, optic nerve and iris abnormalities. Additional common features included hypotonia (61%), heart defects (52%), growth failure (54%), and kidney anomalies (35%). PrediXcan analysis showed that phecodes most strongly associated with reduced predicted PRR12 expression were enriched for eye- (7/30) and kidney- (4/30) phenotypes, such as wet macular degeneration and chronic kidney disease. CONCLUSION: These findings support PRR12 haploinsufficiency as a cause for a novel disorder with a wide clinical spectrum marked chiefly by neurodevelopmental and eye abnormalities.


Subject(s)
Haploinsufficiency , Intellectual Disability , Animals , Haploinsufficiency/genetics , Humans , Intellectual Disability/genetics , Mice , Muscle Hypotonia , Mutation, Missense , Phenotype
20.
Genet Med ; 23(3): 543-554, 2021 03.
Article in English | MEDLINE | ID: mdl-33149277

ABSTRACT

PURPOSE: A few de novo missense variants in the cytoplasmic FMRP-interacting protein 2 (CYFIP2) gene have recently been described as a novel cause of severe intellectual disability, seizures, and hypotonia in 18 individuals, with p.Arg87 substitutions in the majority. METHODS: We assembled data from 19 newly identified and all 18 previously published individuals with CYFIP2 variants. By structural modeling and investigation of WAVE-regulatory complex (WRC)-mediated actin polymerization in six patient fibroblast lines we assessed the impact of CYFIP2 variants on the WRC. RESULTS: Sixteen of 19 individuals harbor two previously described and 11 novel (likely) disease-associated missense variants. We report p.Asp724 as second mutational hotspot (4/19 cases). Genotype-phenotype correlation confirms a consistently severe phenotype in p.Arg87 patients but a more variable phenotype in p.Asp724 and other substitutions. Three individuals with milder phenotypes carry putative loss-of-function variants, which remain of unclear pathogenicity. Structural modeling predicted missense variants to disturb interactions within the WRC or impair CYFIP2 stability. Consistent with its role in WRC-mediated actin polymerization we substantiate aberrant regulation of the actin cytoskeleton in patient fibroblasts. CONCLUSION: Our study expands the clinical and molecular spectrum of CYFIP2-related neurodevelopmental disorder and provides evidence for aberrant WRC-mediated actin dynamics as contributing cellular pathomechanism.


Subject(s)
Intellectual Disability , Neurodevelopmental Disorders , Actins/genetics , Adaptor Proteins, Signal Transducing/metabolism , Humans , Intellectual Disability/genetics , Neurodevelopmental Disorders/genetics , Seizures
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