Variants in SCAF4 Cause a Neurodevelopmental Disorder and Are Associated with Impaired mRNA Processing.

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.

Heterozygous RNF13 Gain-of-Function Variants Are Associated with Congenital Microcephaly, Epileptic Encephalopathy, Blindness, and Failure to Thrive.

Accumulation of unfolded proteins in the endoplasmic reticulum (ER) initiates a stress response mechanism to clear out the unfolded proteins by either facilitating their re-folding or inducing their degradation. When this fails, an apoptotic cascade is initiated so that the affected cell is eliminated. IRE1α is a critical sensor of the unfolded-protein response, essential for initiating the apoptotic signaling. Here, we report an infantile neurodegenerative disorder associated with enhanced activation of IRE1α and increased apoptosis. Three unrelated affected individuals with congenital microcephaly, infantile epileptic encephalopathy, and profound developmental delay were found to carry heterozygous variants (c.932T>C [p.Leu311Ser] or c.935T>C [p.Leu312Pro]) in RNF13, which codes for an IRE1α-interacting protein. Structural modeling predicted that the variants, located on the surface of the protein, would not alter overall protein folding. Accordingly, the abundance of RNF13 and IRE1α was not altered in affected individuals' cells. However, both IRE1α-mediated stress signaling and stress-induced apoptosis were increased in affected individuals' cells. These results indicate that the RNF13 variants confer gain of function to the encoded protein and thereby lead to altered signaling of the ER stress response associated with severe neurodegeneration in infancy.

Clinical and radiographic delineation of Bent Bone Dysplasia-FGFR2 type or Bent Bone Dysplasia with Distinctive Clavicles and Angel-shaped Phalanges.

Bent Bone Dysplasia-FGFR2 type is a relatively recently described bent bone phenotype with diagnostic clinical, radiographic, and molecular characteristics. Here we report on 11 individuals, including the original four patients plus seven new individuals with three longer-term survivors. The prenatal phenotype included stillbirth, bending of the femora, and a high incidence of polyhydramnios, prematurity, and perinatal death in three of 11 patients in the series. The survivors presented with characteristic radiographic findings that were observed among those with lethality, including bent bones, distinctive (moustache-shaped) small clavicles, angel-shaped metacarpals and phalanges, poor mineralization of the calvarium, and craniosynostosis. Craniofacial abnormalities, hirsutism, hepatic abnormalities, and genitourinary abnormalities were noted as well. Longer-term survivors all needed ventilator support. Heterozygosity for mutations in the gene that encodes Fibroblast Growth Factor Receptor 2 (FGFR2) was identified in the nine individuals with available DNA. Description of these patients expands the prenatal and postnatal findings of Bent Bone Dysplasia-FGFR2 type and adds to the phenotypic spectrum among all FGFR2 disorders. © 2016 Wiley Periodicals, Inc.

2q23.1 microdeletion of the MBD5 gene in a female with seizures, developmental delay and distinct dysmorphic features.

We report a 2-year-old female who initially presented with seizures, developmental delay and dysmorphic features and was found to have a 0.3 Mb deletion at chromosome 2q23.1 encompassing the critical seizure gene, MBD5. Her distinct physical features include bifrontal narrowing with brachycephaly, low anterior hairline, hypotonic facial features with short upturned nose, flat nasal bridge, hypertelorism, tented upper lip with everted lower lip, downturned corners of her mouth, and relatively coarse facial features including thickened tongue. She also had a short neck, brachytelephalangy, clinodactyly, and hypertrichosis. At 3½ years she developed progressive ataxia and lost vocabulary at the age of 4. Regression has been reported in one other case of MBD5 deletion. MBD5 is a member of the methyl binding gene family and appears to be responsible for regulating DNA methylation in the central nervous system. Our patient was entirely deleted for the MBD5 gene with partial loss of the EPC2 gene, which suggests that haploinsufficiency of MBD5 is responsible for the distinct phenotype observed. This supports the hypothesis that MBD5 is indeed the critical gene implicated for the findings seen in patients with deletions of chromosome 2q23.1. Further studies are necessary to delineate the role that the MBD5 gene plays in the development of the brain and these specific physical characteristics.

Clinical review of genetic epileptic encephalopathies.

Seizures are a frequently encountered finding in patients seen for clinical genetics evaluations. The differential diagnosis for the cause of seizures is quite diverse and complex, and more than half of all epilepsies have been attributed to a genetic cause. Given the complexity of such evaluations, we highlight the more common causes of genetic epileptic encephalopathies and emphasize the usefulness of recent technological advances. The purpose of this review is to serve as a practical guide for clinical geneticists in the evaluation and counseling of patients with genetic epileptic encephalopathies. Common syndromes will be discussed, in addition to specific seizure phenotypes, many of which are refractory to anti-epileptic agents. Divided by etiology, we overview the more common causes of infantile epileptic encephalopathies, channelopathies, syndromic, metabolic, and chromosomal entities. For each condition, we will outline the diagnostic evaluation and discuss effective treatment strategies that should be considered.

2q23.1 microdeletion of the MBD5 gene in a female with seizures, developmental delay and distinct dysmorphic features.

We report a 2-year-old female who initially presented with seizures, developmental delay and dysmorphic features and was found to have a 0.3 Mb deletion at chromosome 2q23.1 encompassing the critical seizure gene, MBD5. Her distinct physical features include bifrontal narrowing with brachycephaly, low anterior hairline, hypotonic facial features with short upturned nose, flat nasal bridge, hypertelorism, tented upper lip with everted lower lip, downturned corners of her mouth, and relatively coarse facial features including thickened tongue. She also had a short neck, brachytelephalangy, clinodactyly, and hypertrichosis. At 3½ years she developed progressive ataxia and lost vocabulary at the age of 4. Regression has been reported in one other case of MBD5 deletion. MBD5 is a member of the methyl binding gene family and appears to be responsible for regulating DNA methylation in the central nervous system. Our patient was entirely deleted for the MBD5 gene with partial loss of the EPC2 gene, which suggests that haploinsufficiency of MBD5 is responsible for the distinct phenotype observed. This supports the hypothesis that MBD5 is indeed the critical gene implicated for the findings seen in patients with deletions of chromosome 2q23.1. Further studies are necessary to delineate the role that the MBD5 gene plays in the development of the brain and these specific physical characteristics.