@article {941, title = {MED27 Variants Cause Developmental Delay, Dystonia, and Cerebellar Hypoplasia.}, journal = {Ann Neurol}, volume = {89}, year = {2021}, month = {2021 04}, pages = {828-833}, abstract = {

The Mediator multiprotein complex functions as a regulator of RNA polymerase II-catalyzed gene transcription. In this study, exome sequencing detected biallelic putative disease-causing variants in MED27, encoding Mediator complex subunit 27, in 16 patients from 11 families with a novel neurodevelopmental syndrome. Patient phenotypes are highly homogeneous, including global developmental delay, intellectual disability, axial hypotonia with distal spasticity, dystonic movements, and cerebellar hypoplasia. Seizures and cataracts were noted in severely affected individuals. Identification of multiple patients with biallelic MED27 variants supports the critical role of MED27 in normal human neural development, particularly for the cerebellum. ANN NEUROL 2021;89:828-833.

}, keywords = {Adolescent, Adult, Amino Acid Sequence, Cataract, Cerebellum, Child, Child, Preschool, Developmental Disabilities, Dystonia, Epilepsy, Genetic Variation, Humans, Infant, Mediator Complex, Nervous System Malformations, Phenotype, Whole Exome Sequencing}, issn = {1531-8249}, doi = {10.1002/ana.26019}, author = {Meng, Linyan and Isohanni, Pirjo and Shao, Yunru and GrAHm, Brett H and Hickey, Scott E and Brooks, Stephanie and Suomalainen, Anu and Joset, Pascal and Steindl, Katharina and Rauch, Anita and Hackenberg, Annette and High, Frances A and Armstrong-Javors, Amy and Mencacci, Niccol{\`o} E and Gonz{\`a}lez-Latapi, Paulina and Kamel, Walaa A and Al-Hashel, Jasem Y and Bustos, Bernab{\'e} I and Hernandez, Alejandro V and Krainc, Dimitri and Lubbe, Steven J and Van Esch, Hilde and De Luca, Chiara and Ballon, Katleen and Ravelli, Claudia and Burglen, Lydie and Qebibo, Leila and Calame, Daniel G and Mitani, Tadahiro and Marafi, Dana and Pehlivan, Davut and Saadi, Nebal W and Sahin, Yavuz and Maroofian, Reza and Efthymiou, Stephanie and Houlden, Henry and Maqbool, Shazia and Rahman, Fatima and Gu, Shen and Posey, Jennifer E and Lupski, James R and Hunter, Jill V and Wangler, Michael F and Carroll, Christopher J and Yang, Yaping} } @article {738, title = {Deficiencies in vesicular transport mediated by TRAPPC4 are associated with severe syndromic intellectual disability.}, journal = {Brain}, volume = {143}, year = {2020}, month = {2020 01 01}, pages = {112-130}, abstract = {

The conserved transport protein particle (TRAPP) complexes regulate key trafficking events and are required for autophagy. TRAPPC4, like its yeast Trs23 orthologue, is a core component of the TRAPP complexes and one of the essential subunits for guanine nucleotide exchange factor activity for Rab1 GTPase. Pathogenic variants in specific TRAPP subunits are associated with neurological disorders. We undertook exome sequencing in three unrelated families of Caucasian, Turkish and French-Canadian ethnicities with seven affected children that showed features of early-onset seizures, developmental delay, microcephaly, sensorineural deafness, spastic quadriparesis and progressive cortical and cerebellar atrophy in an effort to determine the genetic aetiology underlying neurodevelopmental disorders. All seven affected subjects shared the same identical rare, homozygous, potentially pathogenic variant in a non-canonical, well-conserved splice site within TRAPPC4 (hg19:chr11:g.118890966A>G; TRAPPC4: NM_016146.5; c.454+3A>G). Single nucleotide polymorphism array analysis revealed there was no haplotype shared between the tested Turkish and Caucasian families suggestive of a variant hotspot region rather than a founder effect. In silico analysis predicted the variant to cause aberrant splicing. Consistent with this, experimental evidence showed both a reduction in full-length transcript levels and an increase in levels of a shorter transcript missing exon 3, suggestive of an incompletely penetrant splice defect. TRAPPC4 protein levels were significantly reduced whilst levels of other TRAPP complex subunits remained unaffected. Native polyacrylamide gel electrophoresis and size exclusion chromatography demonstrated a defect in TRAPP complex assembly and/or stability. Intracellular trafficking through the Golgi using the marker protein VSVG-GFP-ts045 demonstrated significantly delayed entry into and exit from the Golgi in fibroblasts derived from one of the affected subjects. Lentiviral expression of wild-type TRAPPC4 in these fibroblasts restored trafficking, suggesting that the trafficking defect was due to reduced TRAPPC4 levels. Consistent with the recent association of the TRAPP complex with autophagy, we found that the fibroblasts had a basal autophagy defect and a delay in autophagic flux, possibly due to unsealed autophagosomes. These results were validated using a yeast trs23 temperature sensitive variant that exhibits constitutive and stress-induced autophagic defects at permissive temperature and a secretory defect at restrictive temperature. In summary we provide strong evidence for pathogenicity of this variant in a member of the core TRAPP subunit, TRAPPC4 that associates with vesicular trafficking and autophagy defects. This is the first report of a TRAPPC4 variant, and our findings add to the growing number of TRAPP-associated neurological disorders.

}, keywords = {Atrophy, Autophagy, Cerebellum, Cerebral Cortex, Child, Child, Preschool, Craniofacial Abnormalities, Deafness, Developmental Disabilities, Epilepsy, Female, Fibroblasts, Hearing Loss, Sensorineural, Humans, Infant, Infant, Newborn, Intellectual Disability, Male, Microcephaly, Microscopy, Fluorescence, Muscle Spasticity, Nerve Tissue Proteins, Neurodevelopmental Disorders, Pedigree, Quadriplegia, RNA Splice Sites, Syndrome, Vesicular Transport Proteins}, issn = {1460-2156}, doi = {10.1093/brain/awz374}, author = {Van Bergen, Nicole J and Guo, Yiran and Al-Deri, Noraldin and Lipatova, Zhanna and Stanga, Daniela and Zhao, Sarah and Murtazina, Rakhilya and Gyurkovska, Valeriya and Pehlivan, Davut and Mitani, Tadahiro and Gezdirici, Alper and Antony, Jayne and Collins, Felicity and Willis, Mary J H and Coban Akdemir, Zeynep H and Liu, Pengfei and Punetha, Jaya and Hunter, Jill V and Jhangiani, Shalini N and Fatih, Jawid M and Rosenfeld, Jill A and Posey, Jennifer E and Gibbs, Richard A and Karaca, Ender and Massey, Sean and Ranasinghe, Thisara G and Sleiman, Patrick and Troedson, Chris and Lupski, James R and Sacher, Michael and Segev, Nava and Hakonarson, Hakon and Christodoulou, John} } @article {823, title = {Dysfunction of the ciliary ARMC9/TOGARAM1 protein module causes Joubert syndrome.}, journal = {J Clin Invest}, volume = {130}, year = {2020}, month = {2020 08 03}, pages = {4423-4439}, abstract = {

Joubert syndrome (JBTS) is a recessive neurodevelopmental ciliopathy characterized by a pathognomonic hindbrain malformation. All known JBTS genes encode proteins involved in the structure or function of primary cilia, ubiquitous antenna-like organelles essential for cellular signal transduction. Here, we used the recently identified JBTS-associated protein armadillo repeat motif-containing 9 (ARMC9) in tandem-affinity purification and yeast 2-hybrid screens to identify a ciliary module whose dysfunction underlies JBTS. In addition to the known JBTS-associated proteins CEP104 and CSPP1, we identified coiled-coil domain containing 66 (CCDC66) and TOG array regulator of axonemal microtubules 1 (TOGARAM1) as ARMC9 interaction partners. We found that TOGARAM1 variants cause JBTS and disrupt TOGARAM1 interaction with ARMC9. Using a combination of protein interaction analyses, characterization of patient-derived fibroblasts, and analysis of CRISPR/Cas9-engineered zebrafish and hTERT-RPE1 cells, we demonstrated that dysfunction of ARMC9 or TOGARAM1 resulted in short cilia with decreased axonemal acetylation and polyglutamylation, but relatively intact transition zone function. Aberrant serum-induced ciliary resorption and cold-induced depolymerization in ARMC9 and TOGARAM1 patient cell lines suggest a role for this new JBTS-associated protein module in ciliary stability.

}, keywords = {Abnormalities, Multiple, Acetylation, Animals, Armadillo Domain Proteins, Cerebellum, Cilia, CRISPR-Cas Systems, Disease Models, Animal, Eye Abnormalities, Humans, Kidney Diseases, Cystic, Peptides, Retina, Zebrafish, Zebrafish Proteins}, issn = {1558-8238}, doi = {10.1172/JCI131656}, author = {Latour, Brooke L and Van De Weghe, Julie C and Rusterholz, Tamara Ds and Letteboer, Stef Jf and Gomez, Arianna and Shaheen, Ranad and Gesemann, Matthias and Karamzade, Arezou and Asadollahi, Mostafa and Barroso-Gil, Miguel and Chitre, Manali and Grout, Megan E and van Reeuwijk, Jeroen and van Beersum, Sylvia Ec and Miller, Caitlin V and Dempsey, Jennifer C and Morsy, Heba and Bamshad, Michael J and Nickerson, Deborah A and Neuhauss, Stephan Cf and Boldt, Karsten and Ueffing, Marius and Keramatipour, Mohammad and Sayer, John A and Alkuraya, Fowzan S and Bachmann-Gagescu, Ruxandra and Roepman, Ronald and Doherty, Dan} } @article {757, title = {Gomez-L{\'o}pez-Hern{\'a}ndez syndrome: A case report with clinical and molecular evaluation and literature review.}, journal = {Am J Med Genet A}, volume = {182}, year = {2020}, month = {2020 07}, pages = {1761-1766}, abstract = {

Gomez-L{\'o}pez-Hern{\'a}ndez syndrome (GLHS) is characterized by rhombencephalosynapsis (RES), alopecia, trigeminal anesthesia and a distinctive phenotype, including brachyturricephaly. It has been suggested that GLHS should be considered as part of the spectrum of RES-associated conditions that include alopecia, trigeminal anesthesia, and craniofacial anomalies, rather than a distinct entity. To the best of our knowledge, 57 patients with GLHS have been described. Despite its first description in 1979, the etiology of this syndrome remains unknown. Here, we describe, to our knowledge, the first case of a patient with GLHS who was molecularly evaluated and had been prenatally exposed to misoprostol. We also reviewed the clinical and morphological features of the patients described to date to better delineate the phenotype and focus on any evidence for adverse pregnancy outcomes or exposure, including teratogens.

}, keywords = {Abnormalities, Multiple, Alopecia, Cerebellum, Child, Child, Preschool, Craniofacial Abnormalities, Female, Growth Disorders, Humans, Magnetic Resonance Imaging, Misoprostol, Neurocutaneous Syndromes, Phenotype, Rhombencephalon, Trigeminal Nerve}, issn = {1552-4833}, doi = {10.1002/ajmg.a.61594}, author = {Perrone, Eduardo and D{\textquoteright}Almeida, V{\^a}nia and de Macena Sobreira, Nara Lygia and de Mello, Claudia Berlim and de Oliveira, Allan Chiaratti and Burlin, St{\^e}nio and Soares, Maria de F{\'a}tima de Faria and Cernach, Mirlene Cec{\'\i}lia Soares Pinho and Alvarez Perez, Ana Beatriz} } @article {770, title = {MN1 C-terminal truncation syndrome is a novel neurodevelopmental and craniofacial disorder with partial rhombencephalosynapsis.}, journal = {Brain}, volume = {143}, year = {2020}, month = {2020 01 01}, pages = {55-68}, abstract = {

MN1 encodes a transcriptional co-regulator without homology to other proteins, previously implicated in acute myeloid leukaemia and development of the palate. Large deletions encompassing MN1 have been reported in individuals with variable neurodevelopmental anomalies and non-specific facial features. We identified a cluster of de novo truncating mutations in MN1 in a cohort of 23 individuals with strikingly similar dysmorphic facial features, especially midface hypoplasia, and intellectual disability with severe expressive language delay. Imaging revealed an atypical form of rhombencephalosynapsis, a distinctive brain malformation characterized by partial or complete loss of the cerebellar vermis with fusion of the cerebellar hemispheres, in 8/10 individuals. Rhombencephalosynapsis has no previously known definitive genetic or environmental causes. Other frequent features included perisylvian polymicrogyria, abnormal posterior clinoid processes and persistent trigeminal artery. MN1 is encoded by only two exons. All mutations, including the recurrent variant p.Arg1295* observed in 8/21 probands, fall in the terminal exon or the extreme 3{\textquoteright} region of exon 1, and are therefore predicted to result in escape from nonsense-mediated mRNA decay. This was confirmed in fibroblasts from three individuals. We propose that the condition described here, MN1 C-terminal truncation (MCTT) syndrome, is not due to MN1 haploinsufficiency but rather is the result of dominantly acting C-terminally truncated MN1 protein. Our data show that MN1 plays a critical role in human craniofacial and brain development, and opens the door to understanding the biological mechanisms underlying rhombencephalosynapsis.

}, keywords = {Abnormalities, Multiple, Adolescent, Basilar Artery, Carotid Arteries, Cerebellar Vermis, Cerebellum, Child, Child, Preschool, Cohort Studies, Comparative Genomic Hybridization, Craniofacial Abnormalities, Female, Fibroblasts, Humans, Imaging, Three-Dimensional, Infant, Intellectual Disability, Language Development Disorders, Magnetic Resonance Imaging, Male, Middle Aged, Mutation, Nervous System Malformations, Nonsense Mediated mRNA Decay, Polymicrogyria, Real-Time Polymerase Chain Reaction, RNA-Seq, Syndrome, Tomography, X-Ray Computed, Trans-Activators, Tumor Suppressor Proteins, Whole Exome Sequencing, Whole Genome Sequencing}, issn = {1460-2156}, doi = {10.1093/brain/awz379}, author = {Mak, Christopher C Y and Doherty, Dan and Lin, Angela E and Vegas, Nancy and Cho, Megan T and Viot, G{\'e}raldine and Dimartino, Cl{\'e}mantine and Weisfeld-Adams, James D and Lessel, Davor and Joss, Shelagh and Li, Chumei and Gonzaga-Jauregui, Claudia and Zarate, Yuri A and Ehmke, Nadja and Horn, Denise and Troyer, Caitlin and Kant, Sarina G and Lee, Youngha and Ishak, Gisele E and Leung, Gordon and Barone Pritchard, Amanda and Yang, Sandra and Bend, Eric G and Filippini, Francesca and Roadhouse, Chelsea and Lebrun, Nicolas and Mehaffey, Michele G and Martin, Pierre-Marie and Apple, Benjamin and Millan, Francisca and Puk, Oliver and Hoffer, Mariette J V and Henderson, Lindsay B and McGowan, Ruth and Wentzensen, Ingrid M and Pei, Steven and Zahir, Farah R and Yu, Mullin and Gibson, William T and Seman, Ann and Steeves, Marcie and Murrell, Jill R and Luettgen, Sabine and Francisco, Elizabeth and Strom, Tim M and Amlie-Wolf, Louise and Kaindl, Angela M and Wilson, William G and Halbach, Sara and Basel-Salmon, Lina and Lev-El, Noa and Denecke, Jonas and Vissers, Lisenka E L M and Radtke, Kelly and Chelly, Jamel and Zackai, Elaine and Friedman, Jan M and Bamshad, Michael J and Nickerson, Deborah A and Reid, Russell R and Devriendt, Koenraad and Chae, Jong-Hee and Stolerman, Elliot and McDougall, Carey and Powis, Z{\"o}e and Bienvenu, Thierry and Tan, Tiong Y and Orenstein, Naama and Dobyns, William B and Shieh, Joseph T and Choi, Murim and Waggoner, Darrel and Gripp, Karen W and Parker, Michael J and Stoler, Joan and Lyonnet, Stanislas and Cormier-Daire, Val{\'e}rie and Viskochil, David and Hoffman, Trevor L and Amiel, Jeanne and Chung, Brian H Y and Gordon, Christopher T} } @article {755, title = {Severe neurodevelopmental disease caused by a homozygous TLK2 variant.}, journal = {Eur J Hum Genet}, volume = {28}, year = {2020}, month = {2020 03}, pages = {383-387}, abstract = {

A distinct neurodevelopmental phenotype characterised mainly by mild motor and language delay and facial dysmorphism, caused by heterozygous de novo or dominant variants in the TLK2 gene has recently been described. All cases reported carried either truncating variants located throughout the gene, or missense changes principally located at the C-terminal end of the protein mostly resulting in haploinsufficiency of TLK2. Through whole exome sequencing, we identified a homozygous missense variant in TLK2 in a patient showing more severe symptoms than those previously described, including cerebellar vermis hypoplasia and West syndrome. Both parents are heterozygous for the variant and clinically unaffected highlighting that recessive variants in TLK2 can also be disease causing and may act through a different pathomechanism.

}, keywords = {Adult, Cerebellum, Child, Developmental Disabilities, Female, Heterozygote, Homozygote, Humans, Infant, Male, Mutation, Missense, Nervous System Malformations, Pedigree, Protein Kinases, Spasms, Infantile}, issn = {1476-5438}, doi = {10.1038/s41431-019-0519-x}, author = {Topf, Ana and Oktay, Yavuz and Balaraju, Sunitha and Yilmaz, Elmasnur and Sonmezler, Ece and Yis, Uluc and Laurie, Steven and Thompson, Rachel and Roos, Andreas and MacArthur, Daniel G and Yaramis, Ahmet and G{\"u}ng{\"o}r, Serdal and Lochm{\"u}ller, Hanns and Hiz, Semra and Horvath, Rita} } @article {490, title = {Variants in EXOSC9 Disrupt the RNA Exosome and Result in Cerebellar Atrophy with Spinal Motor Neuronopathy.}, journal = {Am J Hum Genet}, volume = {102}, year = {2018}, month = {2018 05 03}, pages = {858-873}, abstract = {

The exosome is a conserved multi-protein complex that is essential for correct RNA processing. Recessive variants in exosome components EXOSC3, EXOSC8, and RBM7 cause various constellations of pontocerebellar hypoplasia (PCH), spinal muscular atrophy (SMA), and central nervous system demyelination. Here, we report on four unrelated affected individuals with recessive variants in EXOSC9 and the effect of the variants on the function of the RNA exosome in~vitro in affected individuals{\textquoteright} fibroblasts and skeletal muscle and in~vivo in zebrafish. The clinical presentation was severe, early-onset, progressive SMA-like motor neuronopathy, cerebellar atrophy, and in one affected individual, congenital fractures of the long bones. Three affected individuals of different ethnicity carried the homozygous c.41T>C (p.Leu14Pro) variant, whereas one affected individual was compound heterozygous for c.41T>C (p.Leu14Pro) and c.481C>T (p.Arg161). We detected reduced EXOSC9 in fibroblasts and skeletal muscle and observed a reduction of the whole multi-subunit exosome complex on blue-native polyacrylamide gel electrophoresis. RNA sequencing of fibroblasts and skeletal muscle detected significant >2-fold changes in genes involved in neuronal development and cerebellar and motor neuron degeneration, demonstrating the widespread effect of the variants. Morpholino oligonucleotide knockdown and CRISPR/Cas9-mediated mutagenesis of exosc9 in zebrafish recapitulated aspects of the human phenotype, as they have in other zebrafish models of exosomal disease. Specifically, portions of the cerebellum and hindbrain were absent, and motor neurons failed to develop and migrate properly. In summary, we show that variants in EXOSC9 result in a neurological syndrome combining cerebellar atrophy and spinal motoneuronopathy, thus expanding the list of human exosomopathies.

}, keywords = {Amino Acid Sequence, Animals, Atrophy, Base Sequence, Cerebellum, Child, Preschool, Exosome Multienzyme Ribonuclease Complex, Exosomes, Female, Fibroblasts, Gene Knockdown Techniques, Genetic Variation, Haplotypes, Humans, Infant, Male, Motor Neurons, Muscle, Skeletal, Pedigree, RNA-Binding Proteins, Spinal Cord, Zebrafish}, issn = {1537-6605}, doi = {10.1016/j.ajhg.2018.03.011}, author = {Burns, David T and Donkervoort, Sandra and M{\"u}ller, Juliane S and Knierim, Ellen and Bharucha-Goebel, Diana and Faqeih, Eissa Ali and Bell, Stephanie K and AlFaifi, Abdullah Y and Monies, Dorota and Millan, Francisca and Retterer, Kyle and Dyack, Sarah and MacKay, Sara and Morales-Gonzalez, Susanne and Giunta, Michele and Munro, Benjamin and Hudson, Gavin and Scavina, Mena and Baker, Laura and Massini, Tara C and Lek, Monkol and Hu, Ying and Ezzo, Daniel and Alkuraya, Fowzan S and Kang, Peter B and Griffin, Helen and Foley, A Reghan and Schuelke, Markus and Horvath, Rita and B{\"o}nnemann, Carsten G} } @article {392, title = {Mutations in ARMC9, which Encodes a Basal Body Protein, Cause Joubert Syndrome in Humans and Ciliopathy Phenotypes in Zebrafish.}, journal = {Am J Hum Genet}, volume = {101}, year = {2017}, month = {2017 Jul 06}, pages = {23-36}, abstract = {

Joubert syndrome (JS) is a recessive neurodevelopmental disorder characterized by hypotonia, ataxia, abnormal eye movements, and variable cognitive impairment. It is defined by a distinctive brain malformation known as the "molar tooth sign" on axial MRI. Subsets of affected individuals have malformations such as coloboma, polydactyly, and encephalocele, as well as progressive retinal dystrophy, fibrocystic kidney disease, and liver fibrosis. More than 35 genes have been associated with JS, but in a subset of families the genetic cause remains unknown. All of the gene products localize in and around the primary cilium, making JS a canonical ciliopathy. Ciliopathies are unified by their overlapping clinical features and underlying mechanisms involving ciliary dysfunction. In this work, we identify biallelic rare, predicted-deleterious ARMC9 variants (stop-gain, missense, splice-site, and single-exon deletion) in 11 individuals with JS from 8 families, accounting for approximately 1\% of the disorder. The associated phenotypes range from isolated neurological involvement to JS with retinal dystrophy, additional brain abnormalities (e.g., heterotopia, Dandy-Walker malformation), pituitary insufficiency, and/or synpolydactyly. We show that ARMC9 localizes to the basal body of the cilium and is upregulated during ciliogenesis. Typical ciliopathy phenotypes (curved body shape, retinal dystrophy, coloboma, and decreased cilia) in a CRISPR/Cas9-engineered zebrafish mutant model provide additional support for ARMC9 as a ciliopathy-associated gene. Identifying ARMC9 mutations as a cause of JS takes us one step closer to a full genetic understanding of this important disorder and enables future functional work to define the central biological mechanisms underlying JS and other ciliopathies.

}, keywords = {Abnormalities, Multiple, Animals, Armadillo Domain Proteins, Basal Bodies, Base Sequence, Brain, Cerebellum, Cilia, Ciliopathies, Diagnostic Imaging, Exome, Eye Abnormalities, Genetic Predisposition to Disease, Humans, Kidney Diseases, Cystic, Mutation, Phenotype, Retina, Sequence Analysis, DNA, Up-Regulation, Zebrafish, Zebrafish Proteins}, issn = {1537-6605}, doi = {10.1016/j.ajhg.2017.05.010}, author = {Van De Weghe, Julie C and Rusterholz, Tamara D S and Latour, Brooke and Grout, Megan E and Aldinger, Kimberly A and Shaheen, Ranad and Dempsey, Jennifer C and Maddirevula, Sateesh and Cheng, Yong-Han H and Phelps, Ian G and Gesemann, Matthias and Goel, Himanshu and Birk, Ohad S and Alanzi, Talal and Rawashdeh, Rifaat and Khan, Arif O and Bamshad, Michael J and Nickerson, Deborah A and Neuhauss, Stephan C F and Dobyns, William B and Alkuraya, Fowzan S and Roepman, Ronald and Bachmann-Gagescu, Ruxandra and Doherty, Dan} } @article {493, title = {Mutations in GPAA1, Encoding a GPI Transamidase Complex Protein, Cause Developmental Delay, Epilepsy, Cerebellar Atrophy, and Osteopenia.}, journal = {Am J Hum Genet}, volume = {101}, year = {2017}, month = {2017 Nov 02}, pages = {856-865}, abstract = {

Approximately one in every 200 mammalian proteins is anchored to the cell membrane through a glycosylphosphatidylinositol (GPI) anchor. These proteins play important roles notably in neurological development and function. To date, more than 20 genes have been implicated in the biogenesis of GPI-anchored proteins. GPAA1 (glycosylphosphatidylinositol anchor attachment 1) is an essential component of the transamidase complex along with PIGK, PIGS, PIGT, and PIGU (phosphatidylinositol-glycan biosynthesis classes K, S, T, and U, respectively). This complex orchestrates the attachment of the GPI anchor to the C terminus of precursor proteins in the endoplasmic reticulum. Here, we report bi-allelic mutations in GPAA1 in ten individuals from five families. Using whole-exome sequencing, we identified two frameshift mutations (c.981_993del [p.Gln327Hisfs102] and c.920delG [p.Gly307Alafs11]), one intronic splicing mutation (c.1164+5C>T), and six missense mutations (c.152C>T [p.Ser51Leu], c.160_161delinsAA [p.Ala54Asn], c.527G>C [p.Trp176Ser], c.869T>C [p.Leu290Pro], c.872T>C [p.Leu291Pro], and c.1165G>C [p.Ala389Pro]). Most individuals presented with global developmental delay, hypotonia, early-onset seizures, cerebellar atrophy, and osteopenia. The splicing mutation was found to decrease GPAA1 mRNA. Moreover, flow-cytometry analysis of five available individual samples showed that several GPI-anchored proteins had decreased cell-surface abundance in leukocytes (FLAER, CD16, and CD59) or fibroblasts (CD73 and CD109). Transduction of fibroblasts with a lentivirus encoding the wild-type protein partially rescued the deficiency of GPI-anchored proteins. These findings highlight the role of the transamidase complex in the development and function of the cerebellum and the skeletal system.

}, keywords = {Acyltransferases, Adolescent, Adult, Alleles, Atrophy, Bone Diseases, Metabolic, Cerebellum, Child, Child, Preschool, Developmental Disabilities, Epilepsy, Exome, Female, Fibroblasts, Glycosylphosphatidylinositols, Humans, Male, Membrane Glycoproteins, Muscle Hypotonia, Mutation, Pedigree, RNA, Messenger, Seizures}, issn = {1537-6605}, doi = {10.1016/j.ajhg.2017.09.020}, author = {Nguyen, Thi Tuyet Mai and Murakami, Yoshiko and Sheridan, Eamonn and Ehresmann, Sophie and Rousseau, Justine and St-Denis, Anik and Chai, Guoliang and Ajeawung, Norbert F and Fairbrother, Laura and Reimschisel, Tyler and Bateman, Alexandra and Berry-Kravis, Elizabeth and Xia, Fan and Tardif, Jessica and Parry, David A and Logan, Clare V and Diggle, Christine and Bennett, Christopher P and Hattingh, Louise and Rosenfeld, Jill A and Perry, Michael Scott and Parker, Michael J and Le Deist, Fran{\c c}oise and Zaki, Maha S and Ignatius, Erika and Isohanni, Pirjo and L{\"o}nnqvist, Tuula and Carroll, Christopher J and Johnson, Colin A and Gleeson, Joseph G and Kinoshita, Taroh and Campeau, Philippe M} } @article {14, title = {Biallelic Mutations in TMTC3, Encoding a Transmembrane and TPR-Containing Protein, Lead to Cobblestone Lissencephaly.}, journal = {Am J Hum Genet}, volume = {99}, year = {2016}, month = {2016 Nov 03}, pages = {1181-1189}, abstract = {

Cobblestone lissencephaly (COB) is a severe brain malformation in which overmigration of neurons and glial cells into the arachnoid space results in the formation of cortical dysplasia. COB occurs in a wide range of genetic disorders known as dystroglycanopathies, which are congenital muscular dystrophies associated with brain and eye anomalies and range from Walker-Warburg syndrome to Fukuyama congenital muscular dystrophy. Each of these conditions has been associated with alpha-dystroglycan defects or with mutations in genes encoding basement membrane components, which are known to interact with alpha-dystroglycan. Our screening of a cohort of 25 families with recessive forms of COB identified six families affected by biallelic mutations in TMTC3 (encoding transmembrane and tetratricopeptide repeat containing 3), a gene without obvious functional connections to alpha-dystroglycan. Most affected individuals showed brainstem and cerebellum hypoplasia, as well as ventriculomegaly. However, the minority of the affected individuals had eye defects or elevated muscle creatine phosphokinase, separating the TMTC3 COB phenotype from typical congenital muscular dystrophies. Our data suggest that loss of TMTC3 causes COB with minimal eye or muscle involvement.

}, keywords = {Alleles, Amino Acid Sequence, Basement Membrane, Brain, Carrier Proteins, Cerebellum, Cobblestone Lissencephaly, Developmental Disabilities, Dystroglycans, Eye Abnormalities, Female, Humans, Infant, Male, Membrane Proteins, Mutation, Nervous System Malformations, Neuroglia, Neurons, Pedigree, Phenotype}, issn = {1537-6605}, doi = {10.1016/j.ajhg.2016.09.007}, author = {Jerber, Julie and Zaki, Maha S and Al-Aama, Jumana Y and Rosti, Rasim Ozgur and Ben-Omran, Tawfeg and Dikoglu, Esra and Silhavy, Jennifer L and Caglar, Caner and Musaev, Damir and Albrecht, Beate and Campbell, Kevin P and Willer, Tobias and Almuriekhi, Mariam and {\c C}a{\u g}layan, Ahmet Okay and Vajsar, Jiri and Bilguvar, Kaya and Ogur, Gonul and Abou Jamra, Rami and G{\"u}nel, Murat and Gleeson, Joseph G} } @article {75, title = {Monoallelic and Biallelic Variants in EMC1 Identified in Individuals with Global Developmental Delay, Hypotonia, Scoliosis, and Cerebellar Atrophy.}, journal = {Am J Hum Genet}, volume = {98}, year = {2016}, month = {2016 Mar 03}, pages = {562-570}, abstract = {

The paradigm of a single gene associated with one specific phenotype and mode of inheritance has been repeatedly challenged. Genotype-phenotype correlations can often be traced to different mutation types, localization of the variants in distinct protein domains, or the trigger of or escape from nonsense-mediated decay. Using whole-exome sequencing, we identified homozygous variants in EMC1 that segregated with a phenotype of developmental delay, hypotonia, scoliosis, and cerebellar atrophy in three families. In addition, a de novo heterozygous EMC1 variant was seen in an individual with a similar clinical and MRI imaging phenotype. EMC1 encodes a member of the endoplasmic reticulum (ER)-membrane protein complex (EMC), an evolutionarily conserved complex that has been proposed to have multiple roles in ER-associated degradation, ER-mitochondria tethering, and proper assembly of multi-pass transmembrane proteins. Perturbations of protein folding and organelle crosstalk have been implicated in neurodegenerative processes including cerebellar atrophy. We propose EMC1 as a gene in which either biallelic or monoallelic variants might lead to a syndrome including intellectual disability and preferential degeneration of the cerebellum.

}, keywords = {Adolescent, Alleles, Amino Acid Sequence, Atrophy, Cerebellum, Child, Child, Preschool, Developmental Disabilities, Endoplasmic Reticulum-Associated Degradation, Female, Genetic Association Studies, Genetic Variation, Heterozygote, Humans, Magnetic Resonance Imaging, Male, Molecular Sequence Data, Muscle Hypotonia, Mutation, Pedigree, Protein Folding, Proteins, Scoliosis}, issn = {1537-6605}, doi = {10.1016/j.ajhg.2016.01.011}, author = {Harel, Tamar and Yesil, G{\"o}zde and Bayram, Yavuz and Coban-Akdemir, Zeynep and Charng, Wu-Lin and Karaca, Ender and Al Asmari, Ali and Eldomery, Mohammad K and Hunter, Jill V and Jhangiani, Shalini N and Rosenfeld, Jill A and Pehlivan, Davut and El-Hattab, Ayman W and Saleh, Mohammed A and LeDuc, Charles A and Muzny, Donna and Boerwinkle, Eric and Gibbs, Richard A and Chung, Wendy K and Yang, Yaping and Belmont, John W and Lupski, James R} } @article {55, title = {Mutations in CEP120 cause Joubert syndrome as well as complex ciliopathy phenotypes.}, journal = {J Med Genet}, volume = {53}, year = {2016}, month = {2016 09}, pages = {608-15}, abstract = {

BACKGROUND: Ciliopathies are an extensive group of autosomal recessive or X-linked disorders with considerable genetic and clinical overlap, which collectively share multiple organ involvement and may result in lethal or viable phenotypes. In large numbers of cases the genetic defect remains yet to be determined. The aim of this study is to describe the mutational frequency and phenotypic spectrum of the CEP120 gene.

METHODS: Exome sequencing was performed in 145 patients with Joubert syndrome (JS), including 15 children with oral-facial-digital syndrome type VI (OFDVI) and 21 Meckel syndrome (MKS) fetuses. Moreover, exome sequencing was performed in one fetus with tectocerebellar dysraphia with occipital encephalocele (TCDOE), molar tooth sign and additional skeletal abnormalities. As a parallel study, 346 probands with a phenotype consistent with JS or related ciliopathies underwent next-generation sequencing-based targeted sequencing of 120 previously described and candidate ciliopathy genes.

RESULTS: We present six probands carrying nine distinct mutations (of which eight are novel) in the CEP120 gene, previously found mutated only in Jeune asphyxiating thoracic dystrophy (JATD). The CEP120-associated phenotype ranges from mild classical JS in four patients to more severe conditions in two fetuses, with overlapping features of distinct ciliopathies that include TCDOE, MKS, JATD and OFD syndromes. No obvious correlation is evident between the type or location of identified mutations and the ciliopathy phenotype.

CONCLUSION: Our findings broaden the spectrum of phenotypes caused by CEP120 mutations that account for nearly 1\% of patients with JS as well as for more complex ciliopathy phenotypes. The lack of clear genotype-phenotype correlation highlights the relevance of comprehensive genetic analyses in the diagnostics of ciliopathies.

}, keywords = {Abnormalities, Multiple, Amino Acid Sequence, Cell Cycle Proteins, Cerebellar Diseases, Cerebellum, Child, Ciliopathies, Encephalocele, Eye Abnormalities, Female, Genetic Association Studies, Genetic Predisposition to Disease, Genetic Testing, Humans, Kidney Diseases, Cystic, Male, Mutation, Mutation Rate, Orofaciodigital Syndromes, Pedigree, Phenotype, Retina, Sequence Alignment}, issn = {1468-6244}, doi = {10.1136/jmedgenet-2016-103832}, author = {Roosing, Susanne and Romani, Marta and Isrie, Mala and Rosti, Rasim Ozgur and Micalizzi, Alessia and Musaev, Damir and Mazza, Tommaso and Al-Gazali, Lihadh and Altunoglu, Umut and Boltshauser, Eugen and D{\textquoteright}Arrigo, Stefano and De Keersmaecker, Bart and Kayserili, H{\"u}lya and Brandenberger, Sarah and Kraoua, Ichraf and Mark, Paul R and McKanna, Trudy and Van Keirsbilck, Joachim and Moerman, Philippe and Poretti, Andrea and Puri, Ratna and Van Esch, Hilde and Gleeson, Joseph G and Valente, Enza Maria} } @article {179, title = {Biallelic mutations in SNX14 cause a syndromic form of cerebellar atrophy and lysosome-autophagosome dysfunction.}, journal = {Nat Genet}, volume = {47}, year = {2015}, month = {2015 May}, pages = {528-34}, abstract = {

Pediatric-onset ataxias often present clinically as developmental delay and intellectual disability, with prominent cerebellar atrophy as a key neuroradiographic finding. Here we describe a new clinically distinguishable recessive syndrome in 12 families with cerebellar atrophy together with ataxia, coarsened facial features and intellectual disability, due to truncating mutations in the sorting nexin gene SNX14, encoding a ubiquitously expressed modular PX domain-containing sorting factor. We found SNX14 localized to lysosomes and associated with phosphatidylinositol (3,5)-bisphosphate, a key component of late endosomes/lysosomes. Patient-derived cells showed engorged lysosomes and a slower autophagosome clearance rate upon autophagy induction by starvation. Zebrafish morphants for snx14 showed dramatic loss of cerebellar parenchyma, accumulation of autophagosomes and activation of apoptosis. Our results characterize a unique ataxia syndrome due to biallelic SNX14 mutations leading to lysosome-autophagosome dysfunction.

}, keywords = {Animals, Atrophy, Autophagy, Cerebellar Diseases, Cerebellum, Child, Preschool, Female, Gene Frequency, Humans, Infant, Lod Score, Lysosomal Storage Diseases, Lysosomes, Male, Mutation, Phagosomes, Sorting Nexins, Spinocerebellar Ataxias, Syndrome, Zebrafish}, issn = {1546-1718}, doi = {10.1038/ng.3256}, author = {Akizu, Naiara and Cantagrel, Vincent and Zaki, Maha S and Al-Gazali, Lihadh and Wang, Xin and Rosti, Rasim Ozgur and Dikoglu, Esra and Gelot, Antoinette Bernabe and Rosti, Basak and Vaux, Keith K and Scott, Eric M and Silhavy, Jennifer L and Schroth, Jana and Copeland, Brett and Schaffer, Ashleigh E and Gordts, Philip L S M and Esko, Jeffrey D and Buschman, Matthew D and Field, Seth J and Napolitano, Gennaro and Abdel-Salam, Ghada M and Ozgul, R Koksal and Sag{\i}roglu, Mahmut Samil and Azam, Matloob and Ismail, Samira and Aglan, Mona and Selim, Laila and Mahmoud, Iman G and Abdel-Hadi, Sawsan and Badawy, Amera El and Sadek, Abdelrahim A and Mojahedi, Faezeh and Kayserili, H{\"u}lya and Masri, Amira and Bastaki, Laila and Temtamy, Samia and M{\"u}ller, Ulrich and Desguerre, Isabelle and Casanova, Jean-Laurent and Dursun, Ali and G{\"u}nel, Murat and Gabriel, Stacey B and de Lonlay, Pascale and Gleeson, Joseph G} } @article {181, title = {Exome sequencing identifies a homozygous C5orf42 variant in a Turkish kindred with oral-facial-digital syndrome type VI.}, journal = {Am J Med Genet A}, volume = {167A}, year = {2015}, month = {2015 Sep}, pages = {2132-7}, abstract = {

Oral-facial-digital syndrome type VI (OFDVI) is a rare ciliopathy in the spectrum of Joubert syndrome (JS) and distinguished from other oral-facial-digital syndromes by metacarpal abnormalities with central polydactyly and by a molar tooth sign on cranial MRI. Additional characteristic features include short stature, micrognathia, posteriorly rotated low-set ears, hypertelorism, epicanthal folds, broad nasal tip, tongue hamartoma, upper lip notch, intraoral frenula, cleft lip/palate, and renal anomalies. Recently, novel mutations in C5orf42 were identified in 9 out of 11 OFDVI families. In a subsequent study C5orf42 was found to be mutated in only 2 out of 17 OFDVI probands while 28 patients with a pure JS phenotype also had pathogenic mutations of C5orf42. We report on two affected cousins diagnosed with OFDVI who were born from first degree cousin marriages. Whole exome sequencing (WES) identified a homozygous predicted damaging missense mutation (c.4034A > G; p.Gln1345Arg) in the C5orf42 gene. Our data contribute to the evidence that C5orf42 is one of the causative genes for OFDVI.

}, keywords = {Abnormalities, Multiple, Cerebellar Diseases, Cerebellum, Child, Cleft Palate, Exome, Eye Abnormalities, Female, Genetic Predisposition to Disease, Hamartoma, Homozygote, Humans, Kidney Diseases, Cystic, Magnetic Resonance Imaging, Male, Membrane Proteins, Middle Aged, Mutation, Orofaciodigital Syndromes, Phenotype, Retina, Turkey}, issn = {1552-4833}, doi = {10.1002/ajmg.a.37092}, author = {Bayram, Yavuz and Aydin, Hatip and Gambin, Tomasz and Akdemir, Zeynep Coban and Atik, Mehmed M and Karaca, Ender and Karaman, Ali and Pehlivan, Davut and Jhangiani, Shalini N and Gibbs, Richard A and Lupski, James R} } @article {159, title = {Functional genome-wide siRNA screen identifies KIAA0586 as mutated in Joubert syndrome.}, journal = {Elife}, volume = {4}, year = {2015}, month = {2015 May 30}, pages = {e06602}, abstract = {

Defective primary ciliogenesis or cilium stability forms the basis of human ciliopathies, including Joubert syndrome (JS), with defective cerebellar vermis development. We performed a high-content genome-wide small interfering RNA (siRNA) screen to identify genes regulating ciliogenesis as candidates for JS. We analyzed results with a supervised-learning approach, using SYSCILIA gold standard, Cildb3.0, a centriole siRNA screen and the GTex project, identifying 591 likely candidates. Intersection of this data with whole exome results from 145 individuals with unexplained JS identified six families with predominantly compound heterozygous mutations in KIAA0586. A c.428del base deletion in 0.1\% of the general population was found in trans with a second mutation in an additional set of 9 of 163 unexplained JS patients. KIAA0586 is an orthologue of chick Talpid3, required for ciliogenesis and Sonic hedgehog signaling. Our results uncover a relatively high frequency cause for JS and contribute a list of candidates for future gene discoveries in ciliopathies.

}, keywords = {Abnormalities, Multiple, Cell Cycle Proteins, Cerebellum, Eye Abnormalities, Gene Frequency, Genetic Predisposition to Disease, Genetic Testing, Genome-Wide Association Study, Heterozygote, Humans, Kidney Diseases, Cystic, Mutant Proteins, Retina, RNA, Small Interfering}, issn = {2050-084X}, doi = {10.7554/eLife.06602}, author = {Roosing, Susanne and Hofree, Matan and Kim, Sehyun and Scott, Eric and Copeland, Brett and Romani, Marta and Silhavy, Jennifer L and Rosti, Rasim O and Schroth, Jana and Mazza, Tommaso and Miccinilli, Elide and Zaki, Maha S and Swoboda, Kathryn J and Milisa-Drautz, Joanne and Dobyns, William B and Mikati, Mohamed A and {\.I}ncecik, Faruk and Azam, Matloob and Borgatti, Renato and Romaniello, Romina and Boustany, Rose-Mary and Clericuzio, Carol L and D{\textquoteright}Arrigo, Stefano and Str{\o}mme, Petter and Boltshauser, Eugen and Stanzial, Franco and Mirabelli-Badenier, Marisol and Moroni, Isabella and Bertini, Enrico and Emma, Francesco and Steinlin, Maja and Hildebrandt, Friedhelm and Johnson, Colin A and Freilinger, Michael and Vaux, Keith K and Gabriel, Stacey B and Aza-Blanc, Pedro and Heynen-Genel, Susanne and Ideker, Trey and Dynlacht, Brian D and Lee, Ji Eun and Valente, Enza Maria and Kim, Joon and Gleeson, Joseph G} } @article {155, title = {Joubert syndrome: a model for untangling recessive disorders with extreme genetic heterogeneity.}, journal = {J Med Genet}, volume = {52}, year = {2015}, month = {2015 Aug}, pages = {514-22}, abstract = {

BACKGROUND: Joubert syndrome (JS) is a recessive neurodevelopmental disorder characterised by hypotonia, ataxia, cognitive impairment, abnormal eye movements, respiratory control disturbances and a distinctive mid-hindbrain malformation. JS demonstrates substantial phenotypic variability and genetic heterogeneity. This study provides a comprehensive view of the current genetic basis, phenotypic range and gene-phenotype associations in JS.

METHODS: We sequenced 27 JS-associated genes in 440 affected individuals (375 families) from a cohort of 532 individuals (440 families) with JS, using molecular inversion probe-based targeted capture and next-generation sequencing. Variant pathogenicity was defined using the Combined Annotation Dependent Depletion algorithm with an optimised score cut-off.

RESULTS: We identified presumed causal variants in 62\% of pedigrees, including the first B9D2 mutations associated with JS. 253 different mutations in 23 genes highlight the extreme genetic heterogeneity of JS. Phenotypic analysis revealed that only 34\% of individuals have a {\textquoteright}pure JS{\textquoteright} phenotype. Retinal disease is present in 30\% of individuals, renal disease in 25\%, coloboma in 17\%, polydactyly in 15\%, liver fibrosis in 14\% and encephalocele in 8\%. Loss of CEP290 function is associated with retinal dystrophy, while loss of TMEM67 function is associated with liver fibrosis and coloboma, but we observe no clear-cut distinction between JS subtypes.

CONCLUSIONS: This work illustrates how combining advanced sequencing techniques with phenotypic data addresses extreme genetic heterogeneity to provide diagnostic and carrier testing, guide medical monitoring for progressive complications, facilitate interpretation of genome-wide sequencing results in individuals with a variety of phenotypes and enable gene-specific treatments in the future.

}, keywords = {Abnormalities, Multiple, Cerebellum, Cohort Studies, DNA Mutational Analysis, Eye Abnormalities, Genetic Association Studies, Genetic Heterogeneity, Humans, Kidney Diseases, Cystic, Models, Theoretical, Pedigree, Retina, Sequence Analysis, DNA}, issn = {1468-6244}, doi = {10.1136/jmedgenet-2015-103087}, author = {Bachmann-Gagescu, R and Dempsey, J C and Phelps, I G and O{\textquoteright}Roak, B J and Knutzen, D M and Rue, T C and Ishak, G E and Isabella, C R and Gorden, N and Adkins, J and Boyle, E A and de Lacy, N and O{\textquoteright}Day, D and Alswaid, A and Ramadevi A, Radha and Lingappa, L and Louren{\c c}o, C and Martorell, L and Garcia-Cazorla, {\`A} and Ozy{\"u}rek, H and Halilo{\u g}lu, G and Tuysuz, B and Top{\c c}u, M and Chance, P and Parisi, M A and Glass, I A and Shendure, J and Doherty, D} } @article {154, title = {KIAA0586 is Mutated in Joubert Syndrome.}, journal = {Hum Mutat}, volume = {36}, year = {2015}, month = {2015 Sep}, pages = {831-5}, abstract = {

Joubert syndrome (JS) is a recessive neurodevelopmental disorder characterized by a distinctive mid-hindbrain malformation. JS is part of a group of disorders called ciliopathies based on their overlapping phenotypes and common underlying pathophysiology linked to primary cilium dysfunction. Biallelic mutations in one of 28 genes, all encoding proteins localizing to the primary cilium or basal body, can cause JS. Despite this large number of genes, the genetic cause can currently be determined in about 62\% of individuals with JS. To identify novel JS genes, we performed whole exome sequencing on 35 individuals with JS and found biallelic rare deleterious variants (RDVs) in KIAA0586, encoding a centrosomal protein required for ciliogenesis, in one individual. Targeted next-generation sequencing in a large JS cohort identified biallelic RDVs in eight additional families for an estimated prevalence of 2.5\% (9/366 JS families). All affected individuals displayed JS phenotypes toward the mild end of the spectrum.

}, keywords = {Abnormalities, Multiple, Adolescent, Adult, Alternative Splicing, Brain, Cell Cycle Proteins, Cerebellum, Child, Child, Preschool, DNA Mutational Analysis, Eye Abnormalities, Gene Order, Genetic Association Studies, Humans, Kidney Diseases, Cystic, Magnetic Resonance Imaging, Mutation, Phenotype, Retina, Young Adult}, issn = {1098-1004}, doi = {10.1002/humu.22821}, author = {Bachmann-Gagescu, Ruxandra and Phelps, Ian G and Dempsey, Jennifer C and Sharma, Vivek A and Ishak, Gisele E and Boyle, Evan A and Wilson, Meredith and Marques Louren{\c c}o, Charles and Arslan, Mutluay and Shendure, Jay and Doherty, Dan} } @article {148, title = {An siRNA-based functional genomics screen for the~identification of regulators of ciliogenesis and ciliopathy~genes.}, journal = {Nat Cell Biol}, volume = {17}, year = {2015}, month = {2015 Aug}, pages = {1074-1087}, abstract = {

Defects in primary cilium biogenesis underlie the ciliopathies, a growing group of genetic disorders. We describe a whole-genome siRNA-based reverse genetics screen for defects in biogenesis and/or maintenance of the primary cilium, obtaining a global resource. We identify 112 candidate ciliogenesis and ciliopathy genes, including 44 components of the ubiquitin-proteasome system, 12 G-protein-coupled receptors, and 3 pre-mRNA processing factors (PRPF6, PRPF8 and PRPF31) mutated in autosomal dominant retinitis pigmentosa. The PRPFs localize to the connecting cilium, and PRPF8- and PRPF31-mutated cells have ciliary defects. Combining the screen with exome sequencing data identified recessive mutations in PIBF1, also known as CEP90, and C21orf2, also known as LRRC76, as causes of the ciliopathies Joubert and Jeune syndromes. Biochemical approaches place C21orf2 within key ciliopathy-associated protein modules, offering an explanation for the skeletal and retinal involvement observed in individuals with C21orf2 variants. Our global, unbiased approaches provide insights into ciliogenesis complexity and identify roles for unanticipated pathways in human genetic disease.

}, keywords = {Abnormalities, Multiple, Animals, Caenorhabditis elegans, Cerebellar Diseases, Cerebellum, Cilia, Ciliary Motility Disorders, Databases, Genetic, Ellis-Van Creveld Syndrome, Eye Abnormalities, Genetic Markers, Genetic Predisposition to Disease, Genetic Testing, Genome-Wide Association Study, Genomics, HEK293 Cells, High-Throughput Nucleotide Sequencing, Humans, Kidney Diseases, Cystic, Membrane Proteins, Mice, Inbred C57BL, Mice, Knockout, Mutation, Phenotype, Photoreceptor Cells, Pregnancy Proteins, Proteins, Reproducibility of Results, Retina, RNA Interference, Suppressor Factors, Immunologic, Transfection, Zebrafish}, issn = {1476-4679}, doi = {10.1038/ncb3201}, author = {Wheway, Gabrielle and Schmidts, Miriam and Mans, Dorus A and Szymanska, Katarzyna and Nguyen, Thanh-Minh T and Racher, Hilary and Phelps, Ian G and Toedt, Grischa and Kennedy, Julie and Wunderlich, Kirsten A and Sorusch, Nasrin and Abdelhamed, Zakia A and Natarajan, Subaashini and Herridge, Warren and van Reeuwijk, Jeroen and Horn, Nicola and Boldt, Karsten and Parry, David A and Letteboer, Stef J F and Roosing, Susanne and Adams, Matthew and Bell, Sandra M and Bond, Jacquelyn and Higgins, Julie and Morrison, Ewan E and Tomlinson, Darren C and Slaats, Gisela G and van Dam, Teunis J P and Huang, Lijia and Kessler, Kristin and Giessl, Andreas and Logan, Clare V and Boyle, Evan A and Shendure, Jay and Anazi, Shamsa and Aldahmesh, Mohammed and Al Hazzaa, Selwa and Hegele, Robert A and Ober, Carole and Frosk, Patrick and Mhanni, Aizeddin A and Chodirker, Bernard N and Chudley, Albert E and Lamont, Ryan and Bernier, Francois P and Beaulieu, Chandree L and Gordon, Paul and Pon, Richard T and Donahue, Clem and Barkovich, A James and Wolf, Louis and Toomes, Carmel and Thiel, Christian T and Boycott, Kym M and McKibbin, Martin and Inglehearn, Chris F and Stewart, Fiona and Omran, Heymut and Huynen, Martijn A and Sergouniotis, Panagiotis I and Alkuraya, Fowzan S and Parboosingh, Jillian S and Innes, A Micheil and Willoughby, Colin E and Giles, Rachel H and Webster, Andrew R and Ueffing, Marius and Blacque, Oliver and Gleeson, Joseph G and Wolfrum, Uwe and Beales, Philip L and Gibson, Toby and Doherty, Dan and Mitchison, Hannah M and Roepman, Ronald and Johnson, Colin A} } @article {252, title = {CLP1 founder mutation links tRNA splicing and maturation to cerebellar development and neurodegeneration.}, journal = {Cell}, volume = {157}, year = {2014}, month = {2014 Apr 24}, pages = {651-63}, 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.

}, keywords = {Animals, Brain, Cerebellum, Cleavage And Polyadenylation Specificity Factor, Female, Humans, Male, Mice, Models, Molecular, Neurodegenerative Diseases, Nuclear Proteins, Pedigree, Phosphotransferases, RNA Splicing, RNA, Transfer, Saccharomyces cerevisiae, Transcription Factors, Zebrafish, Zebrafish Proteins}, issn = {1097-4172}, doi = {10.1016/j.cell.2014.03.049}, author = {Schaffer, Ashleigh E and Eggens, Veerle R C and {\c C}a{\u g}layan, Ahmet Okay and Reuter, Miriam S and Scott, Eric and Coufal, Nicole G and Silhavy, Jennifer L and Xue, Yuanchao and Kayserili, H{\"u}lya and Yasuno, Katsuhito and Rosti, Rasim Ozgur and Abdellateef, Mostafa and Caglar, Caner and Kasher, Paul R and Cazemier, J Leonie and Weterman, Marian A and Cantagrel, Vincent and Cai, Na and Zweier, Christiane and Altunoglu, Umut and Satkin, N Bilge and Aktar, Fesih and Tuysuz, Beyhan and Yalcinkaya, Cengiz and Caksen, Huseyin and Bilguvar, Kaya and Fu, Xiang-Dong and Trotta, Christopher R and Gabriel, Stacey and Reis, Andr{\'e} and G{\"u}nel, Murat and Baas, Frank and Gleeson, Joseph G} } @article {278, title = {Mutations in CSPP1 lead to classical Joubert syndrome.}, journal = {Am J Hum Genet}, volume = {94}, year = {2014}, month = {2014 Jan 02}, pages = {80-6}, abstract = {

Joubert syndrome and related disorders (JSRDs) are genetically heterogeneous and characterized by a distinctive mid-hindbrain malformation. Causative mutations lead to primary cilia dysfunction, which often results in variable involvement of other organs such as the liver, retina, and kidney. We identified predicted null mutations in CSPP1 in six individuals affected by classical JSRDs. CSPP1 encodes a protein localized to centrosomes and spindle poles, as well as to the primary cilium. Despite the known interaction between CSPP1 and nephronophthisis-associated proteins, none of the affected individuals in our cohort presented with kidney disease, and further, screening of a large cohort of individuals with nephronophthisis demonstrated no mutations. CSPP1 is broadly expressed in neural tissue, and its encoded protein localizes to the primary cilium in an in~vitro model of human neurogenesis. Here, we show abrogated protein levels and ciliogenesis in affected fibroblasts. Our data thus suggest that CSPP1 is involved in neural-specific functions of primary cilia.

}, keywords = {Abnormalities, Multiple, Brain, Cell Cycle Proteins, Centrosome, Cerebellar Diseases, Cerebellum, Cilia, Cohort Studies, Eye Abnormalities, Fibroblasts, Gene Deletion, Humans, Image Processing, Computer-Assisted, Kidney Diseases, Cystic, Microtubule-Associated Proteins, Polymorphism, Single Nucleotide, Retina}, issn = {1537-6605}, doi = {10.1016/j.ajhg.2013.11.015}, author = {Akizu, Naiara and Silhavy, Jennifer L and Rosti, Rasim Ozgur and Scott, Eric and Fenstermaker, Ali G and Schroth, Jana and Zaki, Maha S and Sanchez, Henry and Gupta, Neerja and Kabra, Madhulika and Kara, Majdi and Ben-Omran, Tawfeg and Rosti, Basak and Guemez-Gamboa, Alicia and Spencer, Emily and Pan, Roger and Cai, Na and Abdellateef, Mostafa and Gabriel, Stacey and Halbritter, Jan and Hildebrandt, Friedhelm and van Bokhoven, Hans and G{\"u}nel, Murat and Gleeson, Joseph G} } @article {309, title = {Mutations in LAMB1 cause cobblestone brain malformation without muscular or ocular abnormalities.}, journal = {Am J Hum Genet}, volume = {92}, year = {2013}, month = {2013 Mar 07}, pages = {468-74}, abstract = {

Cobblestone brain malformation (COB) is a neuronal migration disorder characterized by protrusions of neurons beyond the first cortical layer at the pial surface of the brain. It is usually seen in association with dystroglycanopathy types of congenital muscular dystrophies (CMDs) and ocular abnormalities termed muscle-eye-brain disease. Here we report homozygous deleterious mutations in LAMB1, encoding laminin subunit beta-1, in two families with autosomal-recessive COB. Affected individuals displayed a constellation of brain malformations including cortical gyral and white-matter signal abnormalities, severe cerebellar dysplasia, brainstem hypoplasia, and occipital encephalocele, but they had less apparent ocular or muscular abnormalities than are typically observed in COB. LAMB1 is localized to the pial basement membrane, suggesting that defective connection between radial glial cells and the pial surface mediated by LAMB1 leads to this malformation.

}, keywords = {Basement Membrane, Brain, Cerebellum, Cerebral Cortex, Encephalocele, Female, Genetic Predisposition to Disease, Homozygote, Humans, Laminin, Male, Muscular Dystrophies, Nervous System Malformations, Neuroglia, Neurons, Sequence Deletion, Walker-Warburg Syndrome}, issn = {1537-6605}, doi = {10.1016/j.ajhg.2013.02.005}, author = {Radmanesh, Farid and {\c C}a{\u g}layan, Ahmet Okay and Silhavy, Jennifer L and Yilmaz, Cahide and Cantagrel, Vincent and Omar, Tarek and Rosti, Basak and Kaymak{\c c}alan, Hande and Gabriel, Stacey and Li, Mingfeng and {\v S}estan, Nenad and Bilguvar, Kaya and Dobyns, William B and Zaki, Maha S and G{\"u}nel, Murat and Gleeson, Joseph G} }