Your browser doesn't support javascript.
loading
Show: 20 | 50 | 100
Results 1 - 20 de 59
Filter
Add more filters

Country/Region as subject
Publication year range
1.
Am J Hum Genet ; 110(1): 120-145, 2023 01 05.
Article in English | MEDLINE | ID: mdl-36528028

ABSTRACT

Eukaryotic initiation factor-4A2 (EIF4A2) is an ATP-dependent RNA helicase and a member of the DEAD-box protein family that recognizes the 5' cap structure of mRNAs, allows mRNA to bind to the ribosome, and plays an important role in microRNA-regulated gene repression. Here, we report on 15 individuals from 14 families presenting with global developmental delay, intellectual disability, hypotonia, epilepsy, and structural brain anomalies, all of whom have extremely rare de novo mono-allelic or inherited bi-allelic variants in EIF4A2. Neurodegeneration was predominantly reported in individuals with bi-allelic variants. Molecular modeling predicts these variants would perturb structural interactions in key protein domains. To determine the pathogenicity of the EIF4A2 variants in vivo, we examined the mono-allelic variants in Drosophila melanogaster (fruit fly) and identified variant-specific behavioral and developmental defects. The fruit fly homolog of EIF4A2 is eIF4A, a negative regulator of decapentaplegic (dpp) signaling that regulates embryo patterning, eye and wing morphogenesis, and stem cell identity determination. Our loss-of-function (LOF) rescue assay demonstrated a pupal lethality phenotype induced by loss of eIF4A, which was fully rescued with human EIF4A2 wild-type (WT) cDNA expression. In comparison, the EIF4A2 variant cDNAs failed or incompletely rescued the lethality. Overall, our findings reveal that EIF4A2 variants cause a genetic neurodevelopmental syndrome with both LOF and gain of function as underlying mechanisms.


Subject(s)
Drosophila Proteins , Epilepsy , Intellectual Disability , Neurodevelopmental Disorders , Animals , Humans , Drosophila/genetics , Drosophila melanogaster/genetics , Drosophila melanogaster/metabolism , Drosophila Proteins/genetics , Epilepsy/genetics , Eukaryotic Initiation Factor-4A/genetics , Intellectual Disability/genetics , Muscle Hypotonia/genetics , Neurodevelopmental Disorders/genetics , RNA, Messenger/genetics , RNA, Messenger/metabolism
2.
Am J Hum Genet ; 110(5): 790-808, 2023 05 04.
Article in English | MEDLINE | ID: mdl-37071997

ABSTRACT

SRSF1 (also known as ASF/SF2) is a non-small nuclear ribonucleoprotein (non-snRNP) that belongs to the arginine/serine (R/S) domain family. It recognizes and binds to mRNA, regulating both constitutive and alternative splicing. The complete loss of this proto-oncogene in mice is embryonically lethal. Through international data sharing, we identified 17 individuals (10 females and 7 males) with a neurodevelopmental disorder (NDD) with heterozygous germline SRSF1 variants, mostly de novo, including three frameshift variants, three nonsense variants, seven missense variants, and two microdeletions within region 17q22 encompassing SRSF1. Only in one family, the de novo origin could not be established. All individuals featured a recurrent phenotype including developmental delay and intellectual disability (DD/ID), hypotonia, neurobehavioral problems, with variable skeletal (66.7%) and cardiac (46%) anomalies. To investigate the functional consequences of SRSF1 variants, we performed in silico structural modeling, developed an in vivo splicing assay in Drosophila, and carried out episignature analysis in blood-derived DNA from affected individuals. We found that all loss-of-function and 5 out of 7 missense variants were pathogenic, leading to a loss of SRSF1 splicing activity in Drosophila, correlating with a detectable and specific DNA methylation episignature. In addition, our orthogonal in silico, in vivo, and epigenetics analyses enabled the separation of clearly pathogenic missense variants from those with uncertain significance. Overall, these results indicated that haploinsufficiency of SRSF1 is responsible for a syndromic NDD with ID due to a partial loss of SRSF1-mediated splicing activity.


Subject(s)
Intellectual Disability , Neurodevelopmental Disorders , Child , Female , Male , Developmental Disabilities/genetics , Developmental Disabilities/complications , Haploinsufficiency/genetics , Intellectual Disability/pathology , Mutation, Missense/genetics , Neurodevelopmental Disorders/genetics , Phenotype , Humans
3.
Am J Hum Genet ; 108(10): 2006-2016, 2021 10 07.
Article in English | MEDLINE | ID: mdl-34626583

ABSTRACT

Spermatogenesis-associated 5 like 1 (SPATA5L1) represents an orphan gene encoding a protein of unknown function. We report 28 bi-allelic variants in SPATA5L1 associated with sensorineural hearing loss in 47 individuals from 28 (26 unrelated) families. In addition, 25/47 affected individuals (53%) presented with microcephaly, developmental delay/intellectual disability, cerebral palsy, and/or epilepsy. Modeling indicated damaging effect of variants on the protein, largely via destabilizing effects on protein domains. Brain imaging revealed diminished cerebral volume, thin corpus callosum, and periventricular leukomalacia, and quantitative volumetry demonstrated significantly diminished white matter volumes in several individuals. Immunofluorescent imaging in rat hippocampal neurons revealed localization of Spata5l1 in neuronal and glial cell nuclei and more prominent expression in neurons. In the rodent inner ear, Spata5l1 is expressed in the neurosensory hair cells and inner ear supporting cells. Transcriptomic analysis performed with fibroblasts from affected individuals was able to distinguish affected from controls by principal components. Analysis of differentially expressed genes and networks suggested a role for SPATA5L1 in cell surface adhesion receptor function, intracellular focal adhesions, and DNA replication and mitosis. Collectively, our results indicate that bi-allelic SPATA5L1 variants lead to a human disease characterized by sensorineural hearing loss (SNHL) with or without a nonprogressive mixed neurodevelopmental phenotype.


Subject(s)
Cerebral Palsy/pathology , Epilepsy/pathology , Genetic Predisposition to Disease , Genetic Variation , Hearing Loss/pathology , Intellectual Disability/pathology , Muscle Spasticity/pathology , ATPases Associated with Diverse Cellular Activities/genetics , Adolescent , Adult , Alleles , Animals , Cerebral Palsy/etiology , Cerebral Palsy/metabolism , Child, Preschool , Epilepsy/etiology , Epilepsy/metabolism , Female , Hearing Loss/etiology , Hearing Loss/metabolism , Humans , Infant , Infant, Newborn , Intellectual Disability/etiology , Intellectual Disability/metabolism , Male , Muscle Spasticity/etiology , Muscle Spasticity/metabolism , Rats , Young Adult
4.
Epilepsia ; 65(3): 779-791, 2024 Mar.
Article in English | MEDLINE | ID: mdl-38088023

ABSTRACT

OBJECTIVE: Epilepsy with eyelid myoclonia (EEM) spectrum is a generalized form of epilepsy characterized by eyelid myoclonia with or without absences, eye closure-induced seizures with electroencephalographic paroxysms, and photosensitivity. Based on the specific clinical features, age at onset, and familial occurrence, a genetic cause has been postulated. Pathogenic variants in CHD2, SYNGAP1, NEXMIF, RORB, and GABRA1 have been reported in individuals with photosensitivity and eyelid myoclonia, but whether other genes are also involved, or a single gene is uniquely linked with EEM, or its subtypes, is not yet known. We aimed to dissect the genetic etiology of EEM. METHODS: We studied a cohort of 105 individuals by using whole exome sequencing. Individuals were divided into two groups: EEM- (isolated EEM) and EEM+ (EEM accompanied by intellectual disability [ID] or any other neurodevelopmental/psychiatric disorder). RESULTS: We identified nine variants classified as pathogenic/likely pathogenic in the entire cohort (8.57%); among these, eight (five in CHD2, one in NEXMIF, one in SYNGAP1, and one in TRIM8) were found in the EEM+ subcohort (28.57%). Only one variant (IFIH1) was found in the EEM- subcohort (1.29%); however, because the phenotype of the proband did not fit with published data, additional evidence is needed before considering IFIH1 variants and EEM- an established association. Burden analysis did not identify any single burdened gene or gene set. SIGNIFICANCE: Our results suggest that for EEM, as for many other epilepsies, the identification of a genetic cause is more likely with comorbid ID and/or other neurodevelopmental disorders. Pathogenic variants were mostly found in CHD2, and the association of CHD2 with EEM+ can now be considered a reasonable gene-disease association. We provide further evidence to strengthen the association of EEM+ with NEXMIF and SYNGAP1. Possible new associations between EEM+ and TRIM8, and EEM- and IFIH1, are also reported. Although we provide robust evidence for gene variants associated with EEM+, the core genetic etiology of EEM- remains to be elucidated.


Subject(s)
Epilepsy, Generalized , Epilepsy, Reflex , Myoclonus , Humans , Exome Sequencing , Interferon-Induced Helicase, IFIH1/genetics , Epilepsy, Reflex/genetics , Electroencephalography , Eyelids , Carrier Proteins/genetics , Nerve Tissue Proteins/genetics
5.
BMC Genomics ; 24(1): 206, 2023 Apr 18.
Article in English | MEDLINE | ID: mdl-37072692

ABSTRACT

BACKGROUND: Inherited retinal diseases (IRD) are genetically heterogeneous disorders that cause the dysfunction or loss of photoreceptor cells and ultimately lead to blindness. To date, next-generation sequencing procedures fail to detect pathogenic sequence variants in coding regions of known IRD disease genes in about 30-40% of patients. One of the possible explanations for this missing heritability is the presence of yet unidentified transcripts of known IRD genes. Here, we aimed to define the transcript composition of IRD genes in the human retina by a meta-analysis of publicly available RNA-seq datasets using an ad-hoc designed pipeline. RESULTS: We analysed 218 IRD genes and identified 5,054 transcripts, 3,367 of which were not previously reported. We assessed their putative expression levels and focused our attention on 435 transcripts predicted to account for at least 5% of the expression of the corresponding gene. We looked at the possible impact of the newly identified transcripts at the protein level and experimentally validated a subset of them. CONCLUSIONS: This study provides an unprecedented, detailed overview of the complexity of the human retinal transcriptome that can be instrumental in contributing to the resolution of some cases of missing heritability in IRD patients.


Subject(s)
Retinal Diseases , Transcriptome , Humans , Retina/metabolism , Retinal Diseases/genetics , Retinal Diseases/diagnosis , Retinal Diseases/metabolism , Mutation
6.
Am J Med Genet A ; 191(5): 1350-1354, 2023 05.
Article in English | MEDLINE | ID: mdl-36680497

ABSTRACT

The ubiquitin-specific protease USP9X has been found to play a role in multiple aspects of neural development including processes of neuronal migrations. In males, hemizygous partial loss of function variants in USP9X lead to a clinical phenotype primarily characterized by intellectual disability, hypotonia, speech and language impairment, behavioral disturbances accompanied by additional clinical features with variable expressivity. Structural brain abnormalities are reported in all cases where neuro-imaging was performed. The most common radiological features described include hypoplasia/agenesis of the corpus callosum, widened ventricles, white matter disturbances, and cerebellar hypoplasia. Here we report a child harboring a missense variant in USP9X presenting with the classical neurodevelopmental phenotype and a previously unreported radiological picture of periventricular heterotopia. This case expands the phenotypic landscape of this emergent condition and supports the critical role of USP9X in neuronal migration processes.


Subject(s)
Intellectual Disability , Periventricular Nodular Heterotopia , Humans , Child , Male , Periventricular Nodular Heterotopia/diagnostic imaging , Periventricular Nodular Heterotopia/genetics , Intellectual Disability/diagnosis , Intellectual Disability/genetics , Intellectual Disability/complications , Mutation, Missense , Developmental Disabilities/genetics , Radiography , Ubiquitin Thiolesterase/genetics
7.
Brain ; 145(9): 3308-3327, 2022 09 14.
Article in English | MEDLINE | ID: mdl-35851598

ABSTRACT

Variants in RAC3, encoding a small GTPase RAC3 which is critical for the regulation of actin cytoskeleton and intracellular signal transduction, are associated with a rare neurodevelopmental disorder with structural brain anomalies and facial dysmorphism. We investigated a cohort of 10 unrelated participants presenting with global psychomotor delay, hypotonia, behavioural disturbances, stereotyped movements, dysmorphic features, seizures and musculoskeletal abnormalities. MRI of brain revealed a complex pattern of variable brain malformations, including callosal abnormalities, white matter thinning, grey matter heterotopia, polymicrogyria/dysgyria, brainstem anomalies and cerebellar dysplasia. These patients harboured eight distinct de novo RAC3 variants, including six novel variants (NM_005052.3): c.34G > C p.G12R, c.179G > A p.G60D, c.186_188delGGA p.E62del, c.187G > A p.D63N, c.191A > G p.Y64C and c.348G > C p.K116N. We then examined the pathophysiological significance of these novel and previously reported pathogenic variants p.P29L, p.P34R, p.A59G, p.Q61L and p.E62K. In vitro analyses revealed that all tested RAC3 variants were biochemically and biologically active to variable extent, and exhibited a spectrum of different affinities to downstream effectors including p21-activated kinase 1. We then focused on the four variants p.Q61L, p.E62del, p.D63N and p.Y64C in the Switch II region, which is essential for the biochemical activity of small GTPases and also a variation hot spot common to other Rho family genes, RAC1 and CDC42. Acute expression of the four variants in embryonic mouse brain using in utero electroporation caused defects in cortical neuron morphology and migration ending up with cluster formation during corticogenesis. Notably, defective migration by p.E62del, p.D63N and p.Y64C were rescued by a dominant negative version of p21-activated kinase 1. Our results indicate that RAC3 variants result in morphological and functional defects in cortical neurons during brain development through variant-specific mechanisms, eventually leading to heterogeneous neurodevelopmental phenotypes.


Subject(s)
Neurodevelopmental Disorders , rac GTP-Binding Proteins , Animals , Humans , Mice , Neurodevelopmental Disorders/genetics , Neurodevelopmental Disorders/metabolism , Neurons/metabolism , Phenotype , p21-Activated Kinases/genetics , rac GTP-Binding Proteins/genetics , rac GTP-Binding Proteins/metabolism
8.
Am J Med Genet C Semin Med Genet ; 190(1): 102-108, 2022 03.
Article in English | MEDLINE | ID: mdl-35488810

ABSTRACT

Biallelic loss-of-function (LoF) variants in CENPF gene are responsible for Strømme syndrome, a condition presenting with intestinal atresia, anterior ocular chamber anomalies, and microcephaly. Through an international collaboration, four individuals (three males and one female) carrying CENPF biallelic variants, including two missense variants in homozygous state and four LoF variants, were identified by exome sequencing. All individuals had variable degree of developmental delay/intellectual disability and microcephaly (ranging from -2.9 SDS to -5.6 SDS) and a recognizable pattern of dysmorphic facial features including inverted-V shaped interrupted eyebrows, epicanthal fold, depressed nasal bridge, and pointed chin. Although one of the cases had duodenal atresia, all four individuals did not have the combination of internal organ malformations of Strømme syndrome (intestinal atresia and anterior eye segment abnormalities). Immunofluorescence analysis on skin fibroblasts on one of the four cases with the antibody for ARL13B that decorates primary cilia revealed shorter primary cilia that are consistent with a ciliary defect. This case-series of individuals with biallelic CENPF variants suggests the spectrum of clinical manifestations of the disorder that may be related to CENPF variants is broad and can include phenotypes lacking the cardinal features of Strømme syndrome.


Subject(s)
Chromosomal Proteins, Non-Histone , Intellectual Disability , Intestinal Atresia , Microcephaly , Microfilament Proteins , Chromosomal Proteins, Non-Histone/genetics , Eye Abnormalities , Female , Humans , Intestinal Atresia/genetics , Male , Microcephaly/genetics , Microfilament Proteins/genetics , Mutation/genetics , Phenotype
9.
Hum Mol Genet ; 29(13): 2250-2260, 2020 08 03.
Article in English | MEDLINE | ID: mdl-32533184

ABSTRACT

We investigated the genetic origin of the phenotype displayed by three children from two unrelated Italian families, presenting with a previously unrecognized autosomal recessive disorder that included a severe form of spondylo-epiphyseal dysplasia, sensorineural hearing loss, intellectual disability and Leber congenital amaurosis (SHILCA), as well as some brain anomalies that were visible at the MRI. Autozygome-based analysis showed that these children shared a 4.76 Mb region of homozygosity on chromosome 1, with an identical haplotype. Nonetheless, whole-exome sequencing failed to identify any shared rare coding variants, in this region or elsewhere. We then determined the transcriptome of patients' fibroblasts by RNA sequencing, followed by additional whole-genome sequencing experiments. Gene expression analysis revealed a 4-fold downregulation of the gene NMNAT1, residing indeed in the shared autozygous interval. Short- and long-read whole-genome sequencing highlighted a duplication involving 2 out of the 5 exons of NMNAT1 main isoform (NM_022787.3), leading to the production of aberrant mRNAs. Pathogenic variants in NMNAT1 have been previously shown to cause non-syndromic Leber congenital amaurosis (LCA). However, no patient with null biallelic mutations has ever been described, and murine Nmnat1 knockouts show embryonic lethality, indicating that complete absence of NMNAT1 activity is probably not compatible with life. The rearrangement found in our cases, presumably causing a strong but not complete reduction of enzymatic activity, may therefore result in an intermediate syndromic phenotype with respect to LCA and lethality.


Subject(s)
Hearing Loss, Sensorineural/genetics , Leber Congenital Amaurosis/genetics , Nicotinamide-Nucleotide Adenylyltransferase/genetics , Osteochondrodysplasias/genetics , Adolescent , Animals , Child , Child, Preschool , Disease Models, Animal , Exons/genetics , Genetic Predisposition to Disease , Hearing Loss, Sensorineural/complications , Hearing Loss, Sensorineural/pathology , Humans , Infant , Intellectual Disability , Leber Congenital Amaurosis/complications , Leber Congenital Amaurosis/pathology , Male , Mice , Mutation/genetics , NAD/metabolism , Osteochondrodysplasias/complications , Osteochondrodysplasias/pathology , Pedigree , Retinal Degeneration/genetics , Retinal Degeneration/pathology
10.
Am J Hum Genet ; 105(2): 283-301, 2019 08 01.
Article in English | MEDLINE | ID: mdl-31353023

ABSTRACT

The RNA polymerase II complex (pol II) is responsible for transcription of all ∼21,000 human protein-encoding genes. Here, we describe sixteen individuals harboring de novo heterozygous variants in POLR2A, encoding RPB1, the largest subunit of pol II. An iterative approach combining structural evaluation and mass spectrometry analyses, the use of S. cerevisiae as a model system, and the assessment of cell viability in HeLa cells allowed us to classify eleven variants as probably disease-causing and four variants as possibly disease-causing. The significance of one variant remains unresolved. By quantification of phenotypic severity, we could distinguish mild and severe phenotypic consequences of the disease-causing variants. Missense variants expected to exert only mild structural effects led to a malfunctioning pol II enzyme, thereby inducing a dominant-negative effect on gene transcription. Intriguingly, individuals carrying these variants presented with a severe phenotype dominated by profound infantile-onset hypotonia and developmental delay. Conversely, individuals carrying variants expected to result in complete loss of function, thus reduced levels of functional pol II from the normal allele, exhibited the mildest phenotypes. We conclude that subtle variants that are central in functionally important domains of POLR2A cause a neurodevelopmental syndrome characterized by profound infantile-onset hypotonia and developmental delay through a dominant-negative effect on pol-II-mediated transcription of DNA.


Subject(s)
DNA-Directed RNA Polymerases/genetics , Muscle Hypotonia/pathology , Mutation , Neurodevelopmental Disorders/pathology , Saccharomyces cerevisiae/growth & development , Adolescent , Age of Onset , Child , Child, Preschool , Female , HeLa Cells , Heterozygote , Humans , Male , Muscle Hypotonia/enzymology , Muscle Hypotonia/genetics , Neurodevelopmental Disorders/enzymology , Neurodevelopmental Disorders/genetics , Phenotype , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/metabolism
11.
Am J Hum Genet ; 105(2): 302-316, 2019 08 01.
Article in English | MEDLINE | ID: mdl-31256877

ABSTRACT

Members of a paralogous gene family in which variation in one gene is known to cause disease are eight times more likely to also be associated with human disease. Recent studies have elucidated DHX30 and DDX3X as genes for which pathogenic variant alleles are involved in neurodevelopmental disorders. We hypothesized that variants in paralogous genes encoding members of the DExD/H-box RNA helicase superfamily might also underlie developmental delay and/or intellectual disability (DD and/or ID) disease phenotypes. Here we describe 15 unrelated individuals who have DD and/or ID, central nervous system (CNS) dysfunction, vertebral anomalies, and dysmorphic features and were found to have probably damaging variants in DExD/H-box RNA helicase genes. In addition, these individuals exhibit a variety of other tissue and organ system involvement including ocular, outer ear, hearing, cardiac, and kidney tissues. Five individuals with homozygous (one), compound-heterozygous (two), or de novo (two) missense variants in DHX37 were identified by exome sequencing. We identified ten total individuals with missense variants in three other DDX/DHX paralogs: DHX16 (four individuals), DDX54 (three individuals), and DHX34 (three individuals). Most identified variants are rare, predicted to be damaging, and occur at conserved amino acid residues. Taken together, these 15 individuals implicate the DExD/H-box helicases in both dominantly and recessively inherited neurodevelopmental phenotypes and highlight the potential for more than one disease mechanism underlying these disorders.


Subject(s)
DEAD-box RNA Helicases/genetics , Mutation, Missense , Neoplasm Proteins/genetics , Neurodevelopmental Disorders/genetics , Neurodevelopmental Disorders/pathology , RNA Helicases/genetics , Female , Genetic Association Studies , Humans , Infant , Infant, Newborn , Male , Pedigree , Exome Sequencing
12.
Am J Med Genet A ; 188(10): 3032-3040, 2022 10.
Article in English | MEDLINE | ID: mdl-35876338

ABSTRACT

Hemizygous missense variants in the RPL10 gene encoding a ribosomal unit are responsible for an X-linked syndrome presenting with intellectual disability (ID), autism spectrum disorder, epilepsy, dysmorphic features, and multiple congenital anomalies. Among 15 individuals with RPL10-related disorder reported so far, only one patient had retinitis pigmentosa and microcephaly was observed in approximately half of the cases. By exome sequencing, three Italian and one Spanish male children, from three independent families, were found to carry the same hemizygous novel missense variant p.(Arg32Leu) in RPL10, inherited by their unaffected mother in all cases. The variant, not reported in gnomAD, is located in the 28S rRNA binding region, affecting an evolutionary conserved residue and predicted to disrupt the salt-bridge between Arg32 and Asp28. In addition to features consistent with RPL10-related disorder, all four boys had retinal degeneration and postnatal microcephaly. Pathogenic variants in genes responsible for inherited retinal degenerations were ruled out in all the probands. A novel missense RPL10 variant was detected in four probands with a recurrent phenotype including ID, dysmorphic features, progressive postnatal microcephaly, and retinal anomalies. The presented individuals suggest that retinopathy and postnatal microcephaly are clinical clues of RPL10-related disorder, and at least the retinal defect might be more specific for the p.(Arg32Leu) RPL10 variant, suggesting a specific genotype/phenotype correlation.


Subject(s)
Autism Spectrum Disorder , Intellectual Disability , Microcephaly , Nervous System Malformations , Humans , Intellectual Disability/genetics , Intellectual Disability/pathology , Male , Microcephaly/genetics , Microcephaly/pathology , Phenotype
13.
Am J Med Genet A ; 188(12): 3492-3504, 2022 12.
Article in English | MEDLINE | ID: mdl-36135330

ABSTRACT

Esophageal atresia/tracheoesophageal fistula (EA/TEF) is a life-threatening birth defect that often occurs with other major birth defects (EA/TEF+). Despite advances in genetic testing, a molecular diagnosis can only be made in a minority of EA/TEF+ cases. Here, we analyzed clinical exome sequencing data and data from the DECIPHER database to determine the efficacy of exome sequencing in cases of EA/TEF+ and to identify phenotypic expansions involving EA/TEF. Among 67 individuals with EA/TEF+ referred for clinical exome sequencing, a definitive or probable diagnosis was made in 11 cases for an efficacy rate of 16% (11/67). This efficacy rate is significantly lower than that reported for other major birth defects, suggesting that polygenic, multifactorial, epigenetic, and/or environmental factors may play a particularly important role in EA/TEF pathogenesis. Our cohort included individuals with pathogenic or likely pathogenic variants that affect TCF4 and its downstream target NRXN1, and FANCA, FANCB, and FANCC, which are associated with Fanconi anemia. These cases, previously published case reports, and comparisons to other EA/TEF genes made using a machine learning algorithm, provide evidence in support of a potential pathogenic role for these genes in the development of EA/TEF.


Subject(s)
Esophageal Atresia , Tracheoesophageal Fistula , Humans , Tracheoesophageal Fistula/diagnosis , Tracheoesophageal Fistula/genetics , Tracheoesophageal Fistula/complications , Esophageal Atresia/diagnosis , Esophageal Atresia/genetics , Esophageal Atresia/complications , Exome/genetics , Exome Sequencing
15.
Clin Genet ; 100(5): 607-614, 2021 11.
Article in English | MEDLINE | ID: mdl-34296759

ABSTRACT

Early infantile epileptic encephalopathy 38 (EIEE38, MIM #617020) is caused by biallelic variants in ARV1, encoding a transmembrane protein of the endoplasmic reticulum with a pivotal role in glycosylphosphatidylinositol (GPI) biosynthesis. We ascertained seven new patients from six unrelated families harboring biallelic variants in ARV1, including five novel variants. Affected individuals showed psychomotor delay, hypotonia, early onset refractory seizures followed by regression and specific neuroimaging features. Flow cytometric analysis on patient fibroblasts showed a decrease in GPI-anchored proteins on the cell surface, supporting a lower residual activity of the mutant ARV1 as compared to the wildtype. A rescue assay through the transduction of lentivirus expressing wild type ARV1 cDNA effectively rescued these alterations. This study expands the clinical and molecular spectrum of the ARV1-related encephalopathy, confirming the essential role of ARV1 in GPI biosynthesis and brain function.


Subject(s)
Genetic Association Studies , Genetic Predisposition to Disease , Membrane Proteins/deficiency , Phenotype , Spasms, Infantile/diagnosis , Spasms, Infantile/genetics , Alleles , Amino Acid Substitution , Brain/abnormalities , Carrier Proteins/genetics , DNA Mutational Analysis , Facies , Female , GPI-Linked Proteins/biosynthesis , Genetic Association Studies/methods , Glycosylphosphatidylinositols/metabolism , Humans , Magnetic Resonance Imaging , Male , Membrane Proteins/genetics , Mutation , Pedigree , Pregnancy , Prenatal Diagnosis/methods , Spasms, Infantile/metabolism
16.
Am J Med Genet A ; 182(5): 1259-1262, 2020 05.
Article in English | MEDLINE | ID: mdl-32141180

ABSTRACT

Lateral meningocele syndrome (LMS) is due to specific pathogenic variants in the last exon of NOTCH3 gene. Besides the lateral meningoceles, this condition presents with dysmorphic features, short stature, congenital heart defects, and feeding difficulties. Here, we report a girl with neurosensorial hearing loss, severe gastroesophageal reflux disease, congenital heart defects, multiple renal cysts, kyphosis and left-convex scoliosis, dysmorphic features, and mild developmental delay. Exome sequencing detected the previously unreported de novo loss-of-function variant in exon 33 of NOTCH3 p.(Lys2137fs). Following the identification of the gene defect, MRI of the brain and spine revealed temporal encephaloceles, inner ears anomalies, multiple spinal lateral meningoceles, and intra- and extra-dural arachnoid spinal cysts. This case illustrates the power of reverse phenotyping to establish clinical diagnosis and expands the spectrum of clinical manifestations related to LMS to include inner ear abnormalities and multi-cystic kidney disease.


Subject(s)
Abnormalities, Multiple/genetics , Heart Defects, Congenital/genetics , Meningocele/genetics , Receptor, Notch3/genetics , Abnormalities, Multiple/diagnostic imaging , Abnormalities, Multiple/physiopathology , Brain/diagnostic imaging , Brain/physiopathology , Exons/genetics , Female , Genetic Predisposition to Disease , Heart Defects, Congenital/diagnostic imaging , Heart Defects, Congenital/physiopathology , Humans , Magnetic Resonance Imaging , Meningocele/diagnostic imaging , Meningocele/physiopathology , Phenotype , Spine/diagnostic imaging , Spine/physiopathology , Exome Sequencing
17.
Int J Mol Sci ; 21(17)2020 Aug 29.
Article in English | MEDLINE | ID: mdl-32872468

ABSTRACT

Lipedema is an often underdiagnosed chronic disorder that affects subcutaneous adipose tissue almost exclusively in women, which leads to disproportionate fat accumulation in the lower and upper body extremities. Common comorbidities include anxiety, depression, and pain. The correlation between mood disorder and subcutaneous fat deposition suggests the involvement of steroids metabolism and neurohormones signaling, however no clear association has been established so far. In this study, we report on a family with three patients affected by sex-limited autosomal dominant nonsyndromic lipedema. They had been screened by whole exome sequencing (WES) which led to the discovery of a missense variant p.(Leu213Gln) in AKR1C1, the gene encoding for an aldo-keto reductase catalyzing the reduction of progesterone to its inactive form, 20-α-hydroxyprogesterone. Comparative molecular dynamics simulations of the wild-type vs. variant enzyme, corroborated by a thorough structural and functional bioinformatic analysis, suggest a partial loss-of-function of the variant. This would result in a slower and less efficient reduction of progesterone to hydroxyprogesterone and an increased subcutaneous fat deposition in variant carriers. Overall, our results suggest that AKR1C1 is the first candidate gene associated with nonsyndromic lipedema.


Subject(s)
20-Hydroxysteroid Dehydrogenases/genetics , Exome Sequencing/methods , Lipedema/genetics , Mutation, Missense , 20-Hydroxysteroid Dehydrogenases/chemistry , 20-Hydroxysteroid Dehydrogenases/metabolism , 20-alpha-Dihydroprogesterone/metabolism , Adult , Aged , Female , Humans , Lipedema/metabolism , Loss of Function Mutation , Middle Aged , Models, Molecular , Molecular Dynamics Simulation , Pedigree , Progesterone/metabolism , Protein Conformation
18.
Cerebellum ; 18(5): 972-975, 2019 Oct.
Article in English | MEDLINE | ID: mdl-31410782

ABSTRACT

Spinocerebellar Ataxia 23 (SCAR23) is a newly described condition caused by mutations in TDP2 gene. To date, only four patients from two families have been reported, all carrying the same homozygous mutation. We describe a fifth patient, carrying a novel mutation in the same gene, thus confirming the role of TDP2 mutations in determining the disease and defining the main features SCAR23: pediatric onset ataxia and drug-resistant epilepsy and intellectual disability. We further show the clinical presentation which is associated with the neuroradiological evidence of progressive cerebellar atrophy, giving the evidence that SCAR23 can be classified as a degenerative condition.


Subject(s)
DNA-Binding Proteins/genetics , Drug Resistant Epilepsy/genetics , Intellectual Disability/genetics , Mutation/genetics , Phosphoric Diester Hydrolases/genetics , Spinocerebellar Ataxias/genetics , Adolescent , Drug Resistant Epilepsy/complications , Drug Resistant Epilepsy/diagnostic imaging , Female , Humans , Intellectual Disability/complications , Intellectual Disability/diagnostic imaging , Spinocerebellar Ataxias/complications , Spinocerebellar Ataxias/diagnostic imaging , Exome Sequencing/methods
19.
Am J Hum Genet ; 97(1): 67-74, 2015 Jul 02.
Article in English | MEDLINE | ID: mdl-26054435

ABSTRACT

De novo mutations are recognized both as an important source of genetic variation and as a prominent cause of sporadic disease in humans. Mutations identified as de novo are generally assumed to have occurred during gametogenesis and, consequently, to be present as germline events in an individual. Because Sanger sequencing does not provide the sensitivity to reliably distinguish somatic from germline mutations, the proportion of de novo mutations that occur somatically rather than in the germline remains largely unknown. To determine the contribution of post-zygotic events to de novo mutations, we analyzed a set of 107 de novo mutations in 50 parent-offspring trios. Using four different sequencing techniques, we found that 7 (6.5%) of these presumed germline de novo mutations were in fact present as mosaic mutations in the blood of the offspring and were therefore likely to have occurred post-zygotically. Furthermore, genome-wide analysis of "de novo" variants in the proband led to the identification of 4/4,081 variants that were also detectable in the blood of one of the parents, implying parental mosaicism as the origin of these variants. Thus, our results show that an important fraction of de novo mutations presumed to be germline in fact occurred either post-zygotically in the offspring or were inherited as a consequence of low-level mosaicism in one of the parents.


Subject(s)
Embryo, Mammalian , Genetic Variation/genetics , Genome/genetics , Mosaicism/embryology , Point Mutation/genetics , High-Throughput Nucleotide Sequencing/methods , Humans , Models, Genetic , Polymerase Chain Reaction
20.
Am J Med Genet A ; 176(2): 426-430, 2018 02.
Article in English | MEDLINE | ID: mdl-29230941

ABSTRACT

Myhre syndrome is a rare autosomal dominant disorder caused by a narrow spectrum of missense mutations in the SMAD4 gene. Typical features of this disorder are distinctive facial appearance, deafness, intellectual disability, cardiovascular abnormalities, short stature, short hands and feet, compact build, joint stiffness, and skeletal anomalies. The clinical features generally appear during childhood and become more evident in older patients. Therefore, the diagnosis of this syndrome in the first years of life is challenging. We report a 2-year-old girl diagnosed with Myhre syndrome by whole exome sequencing (WES) that revealed the recurrent p.Ile500Val mutation in the SMAD4 gene. Our patient presented with growth deficiency, dysmorphic features, tetralogy of Fallot, and corectopia (also known as ectopia pupillae). The girl we described is the youngest patient with Myhre syndrome. Moreover, corectopia and tetralogy of Fallot have not been previously reported in this disorder.


Subject(s)
Cryptorchidism/genetics , Growth Disorders/genetics , Hand Deformities, Congenital/genetics , Intellectual Disability/genetics , Pupil Disorders/genetics , Smad4 Protein/genetics , Tetralogy of Fallot/genetics , Abnormalities, Multiple/genetics , Abnormalities, Multiple/physiopathology , Child, Preschool , Cryptorchidism/complications , Cryptorchidism/physiopathology , Facies , Female , Growth Disorders/complications , Growth Disorders/physiopathology , Hand Deformities, Congenital/complications , Hand Deformities, Congenital/physiopathology , Humans , Intellectual Disability/complications , Intellectual Disability/physiopathology , Mutation , Phenotype , Pupil Disorders/physiopathology , Tetralogy of Fallot/complications , Tetralogy of Fallot/physiopathology , Exome Sequencing
SELECTION OF CITATIONS
SEARCH DETAIL