Amber Begtrup

Autosomal-Recessive Mutations in AP3B2, Adaptor-Related Protein Complex 3 Beta 2 Subunit, Cause an Early-Onset Epileptic Encephalopathy with Optic Atrophy

Early-onset epileptic encephalopathy (EOEE) represents a heterogeneous group of severe disorders characterized by seizures, interictal epileptiform activity with a disorganized electroencephalography background, developmental regression or retardation, and onset before 1 year of age. Among a cohort of 57 individuals with epileptic encephalopathy, we ascertained two unrelated affected individuals with EOEE associated with developmental impairment and autosomal-recessive variants in AP3B2 by means of whole-exome sequencing. The targeted sequencing of AP3B2 in 86 unrelated individuals with EOEE led to the identification of an additional family. We gathered five additional families with eight affected individuals through the Matchmaker Exchange initiative by matching autosomal-recessive mutations in AP3B2. Reverse phenotyping of 12 affected individuals from eight families revealed a homogeneous EOEE phenotype characterized by severe developmental delay, poor visual contact with optic atrophy, and postnatal microcephaly. No spasticity, albinism, or hematological symptoms were reported. AP3B2 encodes the neuron-specific subunit of the AP-3 complex. Autosomal-recessive variations of AP3B1, the ubiquitous isoform, cause Hermansky-Pudlak syndrome type 2. The only isoform for the δ subunit of the AP-3 complex is encoded by AP3D1. Autosomal-recessive mutations in AP3D1 cause a severe disorder cumulating the symptoms of the AP3B1 and AP3B2 defects.

REST Final-Exon-Truncating Mutations Cause Hereditary Gingival Fibromatosis

Hereditary gingival fibromatosis (HGF) is the most common genetic form of gingival fibromatosis that develops as a slowly progressive, benign, localized or generalized enlargement of keratinized gingiva. HGF is a genetically heterogeneous disorder and can be transmitted either as an autosomal-dominant or autosomal-recessive trait or appear sporadically. To date, four loci (2p22.1, 2p23.3-p22.3, 5q13-q22, and 11p15) have been mapped to autosomes and one gene (SOS1) has been associated with the HGF trait observed to segregate in a dominant inheritance pattern. Here we report 11 individuals with HGF from three unrelated families. Whole-exome sequencing (WES) revealed three different truncating mutations including two frameshifts and one nonsense variant in RE1-silencing transcription factor (REST) in the probands from all families and further genetic and genomic analyses confirmed the WES-identified findings. REST is a transcriptional repressor that is expressed throughout the body; it has different roles in different cellular contexts, such as oncogenic and tumor-suppressor functions and hematopoietic and cardiac differentiation. Here we show the consequences of germline final-exon-truncating mutations in REST for organismal development and the association with the HGF phenotype.

A recurrent de novo CTBP1 mutation is associated with developmental delay, hypotonia, ataxia, and tooth enamel defects

Exome sequencing is an effective way to identify genetic causes of etiologically heterogeneous conditions such as developmental delay and intellectual disabilities. Using exome sequencing, we have identified four patients with similar phenotypes of developmental delay, intellectual disability, failure to thrive, hypotonia, ataxia, and tooth enamel defects who all have the same de novo R331W missense variant in C-terminal binding protein 1 (CTBP1). CTBP1 is a transcriptional regulator critical for development by coordinating different regulatory pathways. The R331W variant found in these patients is within the C-terminal portion of the PLDLS (Pro-Leu-Asp-Leu-Ser) binding cleft, which is the domain through which CTBP1, interacts with chromatin-modifying enzymes and mediates chromatin-dependent gene repression pathways. This is the first report of mutations within CTBP1 in association with any human disease.

Activating de novo mutations in NFE2L2 encoding NRF2 cause a multisystem disorder

Transcription factor NRF2, encoded by NFE2L2, is the master regulator of defense against stress in mammalian cells. Somatic mutations of NFE2L2 leading to NRF2 accumulation promote cell survival and drug resistance in cancer cells. Here we show that the same mutations as inborn de novo mutations cause an early onset multisystem disorder with failure to thrive, immunodeficiency and neurological symptoms. NRF2 accumulation leads to widespread misregulation of gene expression and an imbalance in cytosolic redox balance. The unique combination of white matter lesions, hypohomocysteinaemia and increased G-6-P-dehydrogenase activity will facilitate early diagnosis and therapeutic intervention of this novel disorder.The NRF2 transcription factor regulates the response to stress in mammalian cells. Here, the authors show that activating mutations in NRF2, commonly found in cancer cells, are found in four patients with a multisystem disorder characterized by immunodeficiency and neurological symptoms.

STAG1 mutations cause a novel cohesinopathy characterised by unspecific syndromic intellectual disability

Background Cohesinopathies are rare neurodevelopmental disorders arising from a dysfunction in the cohesin pathway, which enables chromosome segregation and regulates gene transcription. So far, eight genes from this pathway have been reported in human disease. STAG1 belongs to the STAG subunit of the core cohesin complex, along with five other subunits. This work aimed to identify the phenotype ascribed to STAG1 mutations. Methods Among patients referred for intellectual disability (ID) in genetics departments worldwide, array-comparative genomic hybridisation (CGH), gene panel, whole-exome sequencing or whole-genome sequencing were performed following the local diagnostic standards. Results A mutation in STAG1 was identified in 17 individuals from 16 families, 9 males and 8 females aged 2–33 years. Four individuals harboured a small microdeletion encompassing STAG1; three individuals from two families had an intragenic STAG1 deletion. Six deletions were identified by array-CGH, one by whole-exome sequencing. Whole-exome sequencing found de novo heterozygous missense or frameshift STAG1 variants in eight patients, a panel of genes involved in ID identified a missense and a frameshift variant in two individuals. The 17 patients shared common facial features, with wide mouth and deep-set eyes. Four individuals had mild microcephaly, seven had epilepsy. Conclusions We report an international series of 17 individuals from 16 families presenting with syndromic unspecific ID that could be attributed to a STAG1 deletion or point mutation. This first series reporting the phenotype ascribed to mutation in STAG1 highlights the importance of data sharing in the field of rare disorders.

WDR26 Haploinsufficiency Causes a Recognizable Syndrome of Intellectual Disability, Seizures, Abnormal Gait, and Distinctive Facial Features

We report 15 individuals with de novo pathogenic variants in WDR26. Eleven of the individuals carry loss-of-function mutations, and four harbor missense substitutions. These 15 individuals comprise ten females and five males, and all have intellectual disability with delayed speech, a history of febrile and/or non-febrile seizures, and a wide-based, spastic, and/or stiff-legged gait. These subjects share a set of common facial features that include a prominent maxilla and upper lip that readily reveal the upper gingiva, widely spaced teeth, and a broad nasal tip. Together, these features comprise a recognizable facial phenotype. We compared these features with those of chromosome 1q41q42 microdeletion syndrome, which typically contains WDR26, and noted that clinical features are consistent between the two subsets, suggesting that haploinsufficiency of WDR26 contributes to the pathology of 1q41q42 microdeletion syndrome. Consistent with this, WDR26 loss-of-function single-nucleotide mutations identified in these subjects lead to nonsense-mediated decay with subsequent reduction of RNA expression and protein levels. We derived a structural model of WDR26 and note that missense variants identified in these individuals localize to highly conserved residues of this WD-40-repeat-containing protein. Given that WDR26 mutations have been identified in ∼1 in 2,000 of subjects in our clinical cohorts and that WDR26 might be poorly annotated in exome variant-interpretation pipelines, we would anticipate that this disorder could be more common than currently appreciated.

De novo loss of function mutations in KIAA2022 are associated with epilepsy and neurodevelopmental delay in females

Intellectual disability (ID) affects about 3% of the population and has a male gender bias. Of at least 700 genes currently linked to ID, more than 100 have been identified on the X chromosome, including KIAA2022. KIAA2022 is located on Xq13.3 and is expressed in the developing brain. The protein product of KIAA2022, X‐linked Intellectual Disability Protein Related to Neurite Extension (XPN), is developmentally regulated and is involved in neuronal migration and cell adhesion. The clinical manifestations of loss‐of‐function KIAA2022 mutations have been described previously in 15 males, born from unaffected carrier mothers, but few females. Using whole‐exome sequencing, we identified a cohort of five unrelated female patients with de novo probably gene damaging variants in KIAA2022 and core phenotypic features of ID, developmental delay, epilepsy refractory to treatment, and impaired language, of similar severity as reported for male counterparts. This study supports KIAA2022 as a novel cause of X‐linked dominant ID, and broadens the phenotype for KIAA2022 mutations.

Additional de novo missense genetic variants in NALCN associated with CLIFAHDD syndrome

To the Editor: Sodium leak channel nonselective (NALCN) is a sodium leak, G protein-coupled receptor activated channel that regulates the resting membrane potential and neuronal excitability. Mutations in NALCN have been implicated in a range of neurodevelopmental disorders including autosomal recessive infantile neuroaxonal dystrophy, autosomal recessive intellectual disability (ID), and autosomal dominant congenital contractures of the limbs and face, hypotonia, and developmental delay (OMIM #616266 CLIFAHDD) (1–3). All parents provided informed consent, and the study was reviewed and approved by the Institutional Review Board at Columbia University. We utilized clinical whole-exome sequencing (WES) to identify disease etiologies in a series of 4385 individuals with neurodevelopmental disabilities. Filtering of common SNPs, manual curation, evaluation of predicted effects of rare variants and known function of the genes and associated human conditions, and examination of overlapping phenotypes of individuals with de novo variants in the same gene identified variants in NALCN as likely gene damaging in five probands in the series of 4385 patients (0.11%), one of whom declined to be included herein due to being involved in a different collaboration. We identified and Sanger confirmed three novel missense variants in NALCN in four unrelated patients: c.3448C>G:p.Leu1150Val, c.1733A>G:p.Tyr578Cys, and c.1745A>C p.Tyr582Ser, all of which were de novo. All variants are novel and have not previously been reported in the Exome Aggregation Consortium. Of note, another nucleotide substitution at position 1733, resulting in a different amino acid was previously reported (p.Tyr578Ser) (1). All variants are predicted to be deleterious by in silico models (SIFT, PolyPhen2, CADD, LRT, Mutation Taster, FATHMM, MetaSVM, and Provean). The p.Y578C variant is clinically classified as pathogenic, and the p.L1150V and p.Y582S variants as likely pathogenic. NALCN is a leaky, non-specific, voltage independent sodium channel made up of four homologous domain repeats, each containing six transmembrane spanning segment. All three of the novel variants presented here are within the S5 and S6 domains which form the EEKE sodium ion selectivity filter. All variants are located in highly conserved regions of NALCN as determined by GERP++ conservation scores. Conservation alignment reveals that both nucleotide and amino acids are conserved throughout all species down to zebrafish. The p.Ter578Cys variant affects the same residue previously reported by Chong et al. which resulted in the elimination of the wild type NALCN protein when co-expressed with the p.Tyr578Ser allele (1). The four, unrelated probands share common characteristics of a complex neurodevelopmental phenotype (Table 1 and Supporting information). The two older children (patients 1 and 2) have severe ID, with a non-verbal IQ of <50. The clinical course has been that of a static encephalopathy with no regression. Patients 2 and 4 have had seizures. Brain magnetic resonance imaging (MRI) in two patients demonstrated a small cerebellum, and one patient had a thin corpus callosum. Prenatal history was notable for polyhydramnios in three patients, possibly secondary to decreased swallowing of amniotic fluid by the fetus. Orthopedic issues have been significant in three patients with arthrogryposis and clubbed feet in patients 2, 3 and 4 and a decreased range of motion in all large joints in patient 1. Short stature was observed in all patients as they got older, and currently their height and weight are less than the third centile. Gastrointestinal problems were identified in all patients and included constipation, gastroesophageal reflux disease, gastrostomy tube dependence, and intestinal malrotation. Patients 3 and 4 also have significant respiratory distress with apnea and had a history of ventilator dependence. All patients have dysmorphic facial features including high nasal bridge, midface hypoplasia, small mouth and pursed lips. In summary, we report four patients with intellectual disability, small cerebellum, and contractures with novel, de novo predicted deleterious missense variants in NALCN. De novo missense pathogenic variants in or near the S5 and S6 pore-forming segments of NALCN and that result in a dominant negative effect have been previously implicated as the genetic cause of congenital contractures of the limbs and face, hypotonia, and developmental delay (CLIFAHDD) (1). The phenotypic spectrum represented by the four patients described here and those previously reported by Chong and colleagues suggest a wide variability in clinical presentation caused by pathogenic variants in NALCN.

Mutations in TOP3A Cause a Bloom Syndrome-like Disorder

Bloom syndrome, caused by biallelic mutations in BLM, is characterized by prenatal-onset growth deficiency, short stature, an erythematous photosensitive malar rash, and increased cancer predisposition. Diagnostically, a hallmark feature is the presence of increased sister chromatid exchanges (SCEs) on cytogenetic testing. Here, we describe biallelic mutations in TOP3A in ten individuals with prenatal-onset growth restriction and microcephaly. TOP3A encodes topoisomerase III alpha (TopIIIα), which binds to BLM as part of the BTRR complex, and promotes dissolution of double Holliday junctions arising during homologous recombination. We also identify a homozygous truncating variant in RMI1, which encodes another component of the BTRR complex, in two individuals with microcephalic dwarfism. The TOP3A mutations substantially reduce cellular levels of TopIIIα, and consequently subjects’ cells demonstrate elevated rates of SCE. Unresolved DNA recombination and/or replication intermediates persist into mitosis, leading to chromosome segregation defects and genome instability that most likely explain the growth restriction seen in these subjects and in Bloom syndrome. Clinical features of mitochondrial dysfunction are evident in several individuals with biallelic TOP3A mutations, consistent with the recently reported additional function of TopIIIα in mitochondrial DNA decatenation. In summary, our findings establish TOP3A mutations as an additional cause of prenatal-onset short stature with increased cytogenetic SCEs and implicate the decatenation activity of the BTRR complex in their pathogenesis.

Correction: TANGO2: expanding the clinical phenotype and spectrum of pathogenic variants.

The original version of this Article contained an error in the spelling of the author J. Lawrence Merritt, which was incorrectly given as Lawrence Merritt. This has now been corrected in both the PDF and HTML versions of the Article.