Publications by authors named "Klaas J Wierenga"

47 Publications

Clinical and molecular features of 66 patients with musculocontractural Ehlers-Danlos syndrome caused by pathogenic variants in (mcEDS-).

J Med Genet 2021 Nov 23. Epub 2021 Nov 23.

Department of Dermatology, Keio University School of Medicine, Tokyo, Japan.

Background: Musculocontractural Ehlers-Danlos syndrome is caused by biallelic loss-of-function variants in (mcEDS-) or (mcEDS-). Although 48 patients in 33 families with mcEDS- have been reported, the spectrum of pathogenic variants, accurate prevalence of various manifestations and detailed natural history have not been systematically investigated.

Methods: We collected detailed and comprehensive clinical and molecular information regarding previously reported and newly identified patients with mcEDS- through international collaborations.

Results: Sixty-six patients in 48 families (33 males/females; 0-59 years), including 18 newly reported patients, were evaluated. Japanese was the predominant ethnicity (27 families), associated with three recurrent variants. No apparent genotype-phenotype correlation was noted. Specific craniofacial (large fontanelle with delayed closure, downslanting palpebral fissures and hypertelorism), skeletal (characteristic finger morphologies, joint hypermobility, multiple congenital contractures, progressive talipes deformities and recurrent joint dislocation), cutaneous (hyperextensibility, fine/acrogeria-like/wrinkling palmar creases and bruisability) and ocular (refractive errors) features were observed in most patients (>90%). Large subcutaneous haematomas, constipation, cryptorchidism, hypotonia and motor developmental delay were also common (>80%). Median ages at the initial episode of dislocation or large subcutaneous haematoma were both 6 years. Nine patients died; their median age was 12 years. Several features, including joint and skin characteristics (hypermobility/extensibility and fragility), were significantly more frequent in patients with mcEDS- than in eight reported patients with mcEDS-.

Conclusion: This first international collaborative study of mcEDS- demonstrated that the subtype represents a multisystem disorder with unique set of clinical phenotypes consisting of multiple malformations and progressive fragility-related manifestations; these require lifelong, multidisciplinary healthcare approaches.
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http://dx.doi.org/10.1136/jmedgenet-2020-107623DOI Listing
November 2021

Related Developmental and Epileptic Encephalopathy: Phenotypic and Genotypic Spectrum.

Neurol Genet 2021 Dec 15;7(6):e613. Epub 2021 Nov 15.

Department of Epilepsy Genetics and Personalized Treatment (K.M.J., E.G., C.E.G., A.B., R.S.M., G.R.), The Danish Epilepsy Centre Filadelfia, member of ERN EpiCARE, Dianalund; Institute for Regional Health Research (K.M.J., E.G., A.B., R.S.M), University of Southern Denmark, Odense; Department of Neurology (R.P.W.R.), Maastricht University Medical Centre (MUMC+); Academic Centre for Epileptology Kempenhaeghe/MUMC+ (R.P.W.R.), Maastricht; School for Mental Health and Neuroscience (R.P.W.R.), Maastricht University; Department of Clinical Genetics (M.R.), Maastricht University Medical Center, the Netherlands; APHP, Sorbonne Université (S.W.), Hôpital Armand Trousseau, UF de Génétique Clinique, Centre de Référence Anomalies du Développement et Syndromes Malformatifs, Paris, France; Department of Genetics (B.K., J.B., T.C., C.N.), Pitié-Salpêtrière hospital, APHP, Sorbonne Université, Paris, France; Department of Clinical Genomics (K.J.W.), Mayo Clinic Florida, Jacksonville; Service de Génétique Médicale (B.I., A.P., A.-S.D.-P.), CHU de Nantes; Centre de Référence Anomalies du Développement et Syndromes Malformatifs (L.F., A.G., S.M.), FHU TRANSLAD, CHU Dijon; INSERM UMR1231 (L.F., A.G., S.M., F.T.M.-T., A.V.), GAD team, Université de Bourgogne-Franche Comté, Dijon; Unité Fonctionnelle dInnovation diagnostique des maladies rares (F.T.-M.-T., A.V.), Pôle de Biologie, FHU-TRANSLAD, CHU Dijon Bourgogne; Department of Medical Genetics (C.C., M.W.), Rare Diseases and Personalized Medicine, CHU Montpellier, France; Childrens Hospital Colorado (A.L.), Anschutz Medical Campus, Aurora, CO; Division of Clinical Neuroscience (M.J.E., J.P.A.), Department of Pediatrics, Alberta, Canada; Alberta Childrens Hospital (J.P.A., F.B.), Cumming School of Medicine, University of Calgary, Alberta, Canada; Department of Pediatrics (W.A.-H.), Division of Genetics and Genomics, Boston Childrens Hospital and Harvard Medical School, MA; Instituto de Neurología Infanto Juvenil (B.G.), Neuroinfan; Instituto de Genetica-Hospital Universitario (A.M.), Universidad Nacional de Cuyo; Instituto de Histología y Embriología de Mendoza (IHEM) (L.M.), Universidad Nacional de Cuyo, Mendoza, Argentina; Azienda Ospedaliera Universitaria Pisana (A.O.); Neuropaediatric Section (A.B.), Pediatric Department, Santa Chiara University Hospital, Pisa; Department of Medical Sciences- Pediatric Section (A.S.), University of Ferrara, Italy; CHU Bordeaux (J.V.-G.), Bordeaux, France; West Midlands Regional Genetics Service (J.V.), Birmingham Women's and Children's Hospital, Birmingham, UK; Child Neuropsychiatric Division (S.D., L.G.), Spedali Civili, Brescia, Italy; Institut de Pathologie et de Génétique (IPG) (S.M.), Gosselies, Belgium; Divisions of Child and Adolescent Neurology and Epilepsy (E.W.), Department of Neurology, Mayo Clinic, Rochester, MN; Oxford Centre for Genomic Medicine (S.H., H.S.); Oxford University Hospitals NHS Trust (U.K.), United Kingdom; Blank Children's Developmental Center (N.N.), Unity Point Health, West Des Moines, IA; Sutter Medical Centre (S.A.), Sacramento, CA; Kennedy Krieger Institute (J.S.C.); Johns Hopkins University (S.R.N.), Baltimore, MD; Provincial Medical Genetics Program (A.C.), St. Johns Medical Center, NL, Canada; University Medical Center Utrecht (E.H.B.), Utrecht, the Netherlands; Rush University Medical Center (M.H.L., C.B.), Chicago, IL; Medical Genetic Unit (S.B., D.O.), Maternal and Child Department, Ferrara University Hospital; Medical Science Department (D.O.), Ferrara University; Neonatal Intensive Care Unit (E.B.), Pediatric Section, Department of Medical Sciences, Ferrara University, Italy; Department of Clinical Genetics (C.R.), LUMC, Leiden, the Netherlands; Pediatric Unit, Maternal and Child Department (R.F.), Ferrara University Hospital, Italy; APHP Trousseau (A.A., C.M., D.H.); Service de Neuropédiatrie (D.R., A.I.), Hopital Trousseau, Sorbonne Université, APHP.SU, Paris, France; HudsonAlpha Institute for Biotechnology (D.B.), Huntsville, AL; Department of Pediatrics (D.S., S.K.), Weill Cornell Medicine, New York; Queensland Children's Hospital (D.C.), Brisbane, QL, Australia; Department of Neurology (B.G.), Stichting Epilepsie Instellingen Nederland, Zwolle, the Netherlands; Department of Neurology (O.D.), NYU School of Medicine; Atrium Healths Levine Childrens Hospital (L.A.D.), Charlotte, NC; Phoenix Childrens Hospital (T.G.), the University of Arizona College of Medicine; Division of Child Neurology and Psychiatry (D.P.), Azienda Ospedaliero Universitaria; Neurology and Epileptology Unit (I.C.), Pediatric Department, Brotzu Hospital Trust, Cagliari, Italy; Liverpool Centre for Genomic Medicine (L.G., G.R.), Liverpool Womens NHS Foundation Trust, Liverpool, United Kingdom; U.O. Genetica Medica (C.G.), Policlinico S. Orsola-Malpighi, Bologna, Italy; Department of Children's neurosciences (R.R.S.), Guys and ST. Thomas' NHS foundation trust, London United Kingdom; Department of Child Neuropsychiatry (G.C.), University of Verona, Italy; Christian Medical College (S.Y.), Vellore, India; Neurology Pediatric Unit (F.G.), Pediatric Department, Fernandes Figueira Institute, Fiocruz, Brazil; Royal Childrens Hospital (F.J.L.), Melbourne, Australia; Research & Innovation S.r.l. (D.C.), Padova; Pediatric Neurology Unit (S.O., B.S., F.V.), V. Buzzi Childrens Hospital, Milan, Italy; Department of Paediatrics (A.V.A.), London Health Science Centre/Schulich School of Medicine and Dentisty, University of Western Ontario, London, ON, Canada; Ambry Genetics (K.R.), Aliso Viejo, CA; Advocate Lutheran General Hospital (F.T.), Park Ridge, IL; PPG Pediatric Neurology (A.S.K.), Parkview Health, Fort Wayne, IN; Department of Medical Genetics (C.O.), AP-HP, Necker-Enfants Malades Hospital, Paris, France; Department of Neurology (W.B.), UC Davis, Sacramento, CA; Department of Pediatrics (K.K.), Texas A&M University Medical School, Austin; Leeds General Infirmary (S.H,), United Kingdom; Thompson River Pediatrics (A.F.), Johnstown, CO; Department of Neuropediatrics (S.G.), University Hospital Copenhagen, Denmark; Division of Neurology (F.B., R.W.), Department of Paediatrics, The Hospital for Sick Children, Toronto, Ontario, Canada; Hunter Genetics Unit, Waratah, Australia (A.R.); Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, United Kingdom (N.F., D.H.); KBO-Kinderzentrum München, Munich, Germany (M.S.); Division of Neurology, Epilepsy Neurogenetics Initiative, Childrens Hospital of Philadelphia (J.B., K.L.H., I.H., X.R.O-G, H.D.); Perelman School of Medicine, Philadelphia, PA (J.B.); PURA Syndrome Foundation, Greensborough, Australia (I.H., M.A., D.S.); PURA Syndrome Foundation, Kansas City, MO (I.H., D.S.).

Background And Objectives: Purine-rich element-binding protein A () gene encodes Pur-α, a conserved protein essential for normal postnatal brain development. Recently, a syndrome characterized by intellectual disability, hypotonia, epilepsy, and dysmorphic features was suggested. The aim of this study was to define and expand the phenotypic spectrum of syndrome by collecting data, including EEG, from a large cohort of affected patients.

Methods: Data on unpublished and published cases were collected through the Syndrome Foundation and the literature. Data on clinical, genetic, neuroimaging, and neurophysiologic features were obtained.

Results: A cohort of 142 patients was included. Characteristics of the syndrome included neonatal hypotonia, feeding difficulties, and respiratory distress. Sixty percent of the patients developed epilepsy with myoclonic, generalized tonic-clonic, focal seizures, and/or epileptic spasms. EEG showed generalized, multifocal, or focal epileptic abnormalities. Lennox-Gastaut was the most common epilepsy syndrome. Drug refractoriness was common: 33.3% achieved seizure freedom. We found 97 pathogenic variants in without any clear genotype-phenotype associations.

Discussion: The syndrome presents with a developmental and epileptic encephalopathy with characteristics recognizable from neonatal age, which should prompt genetic screening. Sixty percent have drug-resistant epilepsy with focal or generalized seizures. We collected more than 90 pathogenic variants without observing overt genotype-phenotype associations.
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http://dx.doi.org/10.1212/NXG.0000000000000613DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8592566PMC
December 2021

Clinicoradiographic and genetic features of cerebral small vessel disease indicate variability in mode of inheritance for monoallelic HTRA1 variants.

Mol Genet Genomic Med 2021 Oct 12;9(10):e1799. Epub 2021 Sep 12.

Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA.

Background: Biallelic pathogenic variants in HTRA1 cause CARASIL. More recently, monoallelic variants have been associated with the autosomal dominant disorder CADASIL2 but not all carriers develop disease manifestations. We describe the clinicoradiologic and mutation spectrum of four new CADASIL2 individuals.

Methods: Medical records at Mayo Clinic between 2013 and 2020 were retrospectively reviewed to identify patients with cerebral small vessel disease related to monoallelic HTRA1 variants.

Results: Four patients met the study inclusion criteria for cerebral small vessel disease related to HTRA1 monoallelic variants. The mean age at onset of first clinical stroke was 51.25 years (range 41-64 years). The mean disease duration was 6.5 years (range 4-12). All individuals had recurrent strokes within the duration of follow-up with a mean number of strokes per patient being 5.5 (range 2-12). Three individuals had leukoencephalopathy with brain stem involvement. Microhemorrhages were seen on brain MRI in three patients. HTRA1 monoallelic variants identified in our cohort were missense variants in three patients and a novel frameshift variation in one patient. Interestingly, two of these missense variants were previously reported in an autosomal recessive pattern of inheritance and here are associated with a dominant effect.

Conclusions: Clinicoradiologic characteristics of heterozygous HTRA1-related CSVD may overlap with sporadic CSVD. Heterozygous HTRA1 variants can contribute to dominant or recessive disease mechanisms.
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http://dx.doi.org/10.1002/mgg3.1799DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8580093PMC
October 2021

Urine levels of the polyglutamine ataxin-3 protein are elevated in patients with spinocerebellar ataxia type 3.

Parkinsonism Relat Disord 2021 Aug 17;89:151-154. Epub 2021 Jul 17.

Department of Neuroscience, Mayo Clinic, Jacksonville, FL, 32224, USA; Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, 32224, USA. Electronic address:

Introduction: Accumulation of polyglutamine (polyQ) ataxin-3 (ATXN3) contributes to the pathobiology of spinocerebellar ataxia type 3 (SCA3). Recently, we showed that polyQ ATXN3 is elevated in the plasma and cerebrospinal fluid (CSF) of SCA3 patients, and has the potential to serve as a biological marker for this disease [1]. Based on these findings, we investigated whether polyQ ATXN3 can also be detected in urine samples from SCA3 patients.

Methods: We analyzed urine samples from 30 SCA3 subjects (including one pre-symptomatic subject), 35 subjects with other forms of ataxia, and 37 healthy controls. To quantify polyQ ATXN3 protein levels, we used our previously developed immunoassay.

Results: PolyQ ATXN3 can be detected in the urine of SCA3 patients, but not in urine samples from healthy controls or other forms of ataxia. There was a significant statistical association between polyQ ATXN3 levels in urine samples and those in plasma. Further, the levels of polyQ ATXN3 urine associated with an earlier age of SCA3 disease onset.

Conclusion: As clinical trials for SCA3 advance, urine polyQ ATXN3 protein has potential to be a useful, non-invasive and inexpensive biomarker for SCA3.
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http://dx.doi.org/10.1016/j.parkreldis.2021.07.018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8429134PMC
August 2021

Histone H3.3 beyond cancer: Germline mutations in cause a previously unidentified neurodegenerative disorder in 46 patients.

Sci Adv 2020 Dec 2;6(49). Epub 2020 Dec 2.

Institut für Neurogenomik, Helmholtz Zentrum München, Munich, Germany.

Although somatic mutations in Histone 3.3 (H3.3) are well-studied drivers of oncogenesis, the role of germline mutations remains unreported. We analyze 46 patients bearing de novo germline mutations in histone 3 family 3A () or with progressive neurologic dysfunction and congenital anomalies without malignancies. Molecular modeling of all 37 variants demonstrated clear disruptions in interactions with DNA, other histones, and histone chaperone proteins. Patient histone posttranslational modifications (PTMs) analysis revealed notably aberrant local PTM patterns distinct from the somatic lysine mutations that cause global PTM dysregulation. RNA sequencing on patient cells demonstrated up-regulated gene expression related to mitosis and cell division, and cellular assays confirmed an increased proliferative capacity. A zebrafish model showed craniofacial anomalies and a defect in Foxd3-derived glia. These data suggest that the mechanism of germline mutations are distinct from cancer-associated somatic histone mutations but may converge on control of cell proliferation.
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http://dx.doi.org/10.1126/sciadv.abc9207DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7821880PMC
December 2020

Mutations in Spliceosomal Genes PPIL1 and PRP17 Cause Neurodegenerative Pontocerebellar Hypoplasia with Microcephaly.

Neuron 2021 01 20;109(2):241-256.e9. Epub 2020 Nov 20.

Division of Molecular Medicine, Leeds Institute of Medical Research, University of Leeds, Leeds LS9 7TF, UK.

Autosomal-recessive cerebellar hypoplasia and ataxia constitute a group of heterogeneous brain disorders caused by disruption of several fundamental cellular processes. Here, we identified 10 families showing a neurodegenerative condition involving pontocerebellar hypoplasia with microcephaly (PCHM). Patients harbored biallelic mutations in genes encoding the spliceosome components Peptidyl-Prolyl Isomerase Like-1 (PPIL1) or Pre-RNA Processing-17 (PRP17). Mouse knockouts of either gene were lethal in early embryogenesis, whereas PPIL1 patient mutation knockin mice showed neuron-specific apoptosis. Loss of either protein affected splicing integrity, predominantly affecting short and high GC-content introns and genes involved in brain disorders. PPIL1 and PRP17 form an active isomerase-substrate interaction, but we found that isomerase activity is not critical for function. Thus, we establish disrupted splicing integrity and "major spliceosome-opathies" as a new mechanism underlying PCHM and neurodegeneration and uncover a non-enzymatic function of a spliceosomal proline isomerase.
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http://dx.doi.org/10.1016/j.neuron.2020.10.035DOI Listing
January 2021

Impact of integrated translational research on clinical exome sequencing.

Genet Med 2021 03 4;23(3):498-507. Epub 2020 Nov 4.

Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA.

Purpose: Exome sequencing often identifies pathogenic genetic variants in patients with undiagnosed diseases. Nevertheless, frequent findings of variants of uncertain significance necessitate additional efforts to establish causality before reaching a conclusive diagnosis. To provide comprehensive genomic testing to patients with undiagnosed disease, we established an Individualized Medicine Clinic, which offered clinical exome testing and included a Translational Omics Program (TOP) that provided variant curation, research activities, or research exome sequencing.

Methods: From 2012 to 2018, 1101 unselected patients with undiagnosed diseases received exome testing. Outcomes were reviewed to assess impact of the TOP and patient characteristics on diagnostic rates through descriptive and multivariate analyses.

Results: The overall diagnostic yield was 24.9% (274 of 1101 patients), with 174 (15.8% of 1101) diagnosed on the basis of clinical exome sequencing alone. Four hundred twenty-three patients with nondiagnostic or without access to clinical exome sequencing were evaluated by the TOP, with 100 (9% of 1101) patients receiving a diagnosis, accounting for 36.5% of the diagnostic yield. The identification of a genetic diagnosis was influenced by the age at time of testing and the disease phenotype of the patient.

Conclusion: Integration of translational research activities into clinical practice of a tertiary medical center can significantly increase the diagnostic yield of patients with undiagnosed disease.
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http://dx.doi.org/10.1038/s41436-020-01005-9DOI Listing
March 2021

Toward allele-specific targeting therapy and pharmacodynamic marker for spinocerebellar ataxia type 3.

Sci Transl Med 2020 10;12(566)

Department of Pathology, Brain Research Institute, Niigata University, Niigata 951-8585, Japan.

Spinocerebellar ataxia type 3 (SCA3), caused by a CAG repeat expansion in the ataxin-3 gene (), is characterized by neuronal polyglutamine (polyQ) ATXN3 protein aggregates. Although there is no cure for SCA3, gene-silencing approaches to reduce toxic polyQ ATXN3 showed promise in preclinical models. However, a major limitation in translating putative treatments for this rare disease to the clinic is the lack of pharmacodynamic markers for use in clinical trials. Here, we developed an immunoassay that readily detects polyQ ATXN3 proteins in human biological fluids and discriminates patients with SCA3 from healthy controls and individuals with other ataxias. We show that polyQ ATXN3 serves as a marker of target engagement in human fibroblasts, which may bode well for its use in clinical trials. Last, we identified a single-nucleotide polymorphism that strongly associates with the expanded allele, thus providing an exciting drug target to abrogate detrimental events initiated by mutant ATXN3. Gene-silencing strategies for several repeat diseases are well under way, and our results are expected to improve clinical trial preparedness for SCA3 therapies.
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http://dx.doi.org/10.1126/scitranslmed.abb7086DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7927160PMC
October 2020

The expanding LARS2 phenotypic spectrum: HLASA, Perrault syndrome with leukodystrophy, and mitochondrial myopathy.

Hum Mutat 2020 08;41(8):1425-1434

Discipline of Child & Adolescent Health, Sydney Medical School, Sydney, Australia.

LARS2 variants are associated with Perrault syndrome, characterized by premature ovarian failure and hearing loss, and with an infantile lethal multisystem disorder: Hydrops, lactic acidosis, sideroblastic anemia (HLASA) in one individual. Recently we reported LARS2 deafness with (ovario) leukodystrophy. Here we describe five patients with a range of phenotypes, in whom we identified biallelic LARS2 variants: three patients with a HLASA-like phenotype, an individual with Perrault syndrome whose affected siblings also had leukodystrophy, and an individual with a reversible mitochondrial myopathy, lactic acidosis, and developmental delay. Three HLASA cases from two unrelated families were identified. All were males with genital anomalies. Two survived multisystem disease in the neonatal period; both have developmental delay and hearing loss. A 55-year old male with deafness has not displayed neurological symptoms while his female siblings with Perrault syndrome developed leukodystrophy and died in their 30s. Analysis of muscle from a child with a reversible myopathy showed reduced LARS2 and mitochondrial complex I levels, and an unusual form of degeneration. Analysis of recombinant LARS2 variant proteins showed they had reduced aminoacylation efficiency, with HLASA-associated variants having the most severe effect. A broad phenotypic spectrum should be considered in association with LARS2 variants.
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http://dx.doi.org/10.1002/humu.24050DOI Listing
August 2020

mutated acute myeloid leukemia in a child with metaphyseal chondromatosis with D-2-hydroxyglutaric aciduria.

Pediatr Hematol Oncol 2020 Aug 13;37(5):431-437. Epub 2020 Mar 13.

Jimmy Everest Section of Pediatric Hematology/Oncology, Department of Pediatrics, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA.

D-2-hydroxyglutaric aciduria (D-2-HGA) is a rare metabolic disorder characterized by developmental delay, hypotonia, and bi-allelic mutations in D-2-hydroxyglutarate dehydrogenase or a single gain-of-function mutation in isocitrate dehydrogenase 2 Metaphyseal chondromatosis with D-2-hydroxyglutaric aciduria (MC-HGA) is a type of D-2-HGA that has been previously reported in ten patients (OMIM 614875), three of whom had somatic mosaicism for R132 variants in isocitrate dehydrogenase 1 (). We describe a 3-year-old boy with MC-HGA who subsequently developed acute myeloid leukemia (AML) and was found to have an R132C mutation in a leukemic bone marrow sample. Further testing revealed presence of somatic mosaicism for R132C variant, suggesting an association of in inducing myeloid leukemogenesis.
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http://dx.doi.org/10.1080/08880018.2020.1737284DOI Listing
August 2020

Functional Analysis of the SIM1 Variant p.G715V in 2 Patients With Obesity.

J Clin Endocrinol Metab 2020 01;105(1)

Department of Clinical Genomics, Mayo Clinic, Jacksonville, Florida.

Context: Single-minded homologue 1 (SIM1) is a transcription factor with several physiological and developmental functions. Haploinsufficiency of SIM1 is associated with early-onset obesity with or without Prader-Willi-like (PWL) features and may exhibit incomplete penetrance.

Case Description: Next-generation sequencing was performed for 2 male patients with obesity, including 1 man presenting with intellectual disability (ID), body mass index (BMI) of 47.4, and impulse-control disorder, and the other man with early obesity (BMI of 36); sequencing revealed a missense variant in SIM1 (c.2144G>T; p.G715V) in both individuals. Previous studies have identified several disease-associated variants that fall near the p.G715V variant within the C-terminal domain of SIM1. We examined p.G715V variant stability and activity in a doxycycline-inducible stable cell line transfected with an artificial reporter construct and either ARNT or ARNT2 as a partner protein.

Conclusions: Functional testing of the p.G715V variant revealed a significant reduction in SIM1-mediated transcriptional activity. We also generated the first ab initio hybrid protein model for full-length SIM1 to show the predicted spatial relationship between p.G715V and other previously described variants in this region and identified a putative mutation hotspot within the C-terminus. Significant clinical heterogeneity has been observed in patients with SIM1 variants, particularly with regards to the PWL phenotype. In the patient with ID, a second variant of uncertain significance in CHD2 was identified that may contribute to his ID and behavioral disturbances, emphasizing the role of additional genetic modifiers.
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http://dx.doi.org/10.1210/clinem/dgz192DOI Listing
January 2020

Loss of Oxidation Resistance 1, OXR1, Is Associated with an Autosomal-Recessive Neurological Disease with Cerebellar Atrophy and Lysosomal Dysfunction.

Am J Hum Genet 2019 12 27;105(6):1237-1253. Epub 2019 Nov 27.

Centre Hospitalier Universitaire Saint-Justine Research Center, CHU Sainte-Justine, Montreal, QC H3T 1J4, Canada. Electronic address:

We report an early-onset autosomal-recessive neurological disease with cerebellar atrophy and lysosomal dysfunction. We identified bi-allelic loss-of-function (LoF) variants in Oxidative Resistance 1 (OXR1) in five individuals from three families; these individuals presented with a history of severe global developmental delay, current intellectual disability, language delay, cerebellar atrophy, and seizures. While OXR1 is known to play a role in oxidative stress resistance, its molecular functions are not well established. OXR1 contains three conserved domains: LysM, GRAM, and TLDc. The gene encodes at least six transcripts, including some that only consist of the C-terminal TLDc domain. We utilized Drosophila to assess the phenotypes associated with loss of mustard (mtd), the fly homolog of OXR1. Strong LoF mutants exhibit late pupal lethality or pupal eclosion defects. Interestingly, although mtd encodes 26 transcripts, severe LoF and null mutations can be rescued by a single short human OXR1 cDNA that only contains the TLDc domain. Similar rescue is observed with the TLDc domain of NCOA7, another human homolog of mtd. Loss of mtd in neurons leads to massive cell loss, early death, and an accumulation of aberrant lysosomal structures, similar to what we observe in fibroblasts of affected individuals. Our data indicate that mtd and OXR1 are required for proper lysosomal function; this is consistent with observations that NCOA7 is required for lysosomal acidification.
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http://dx.doi.org/10.1016/j.ajhg.2019.11.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6904826PMC
December 2019

A neonate with mucolipidosis II and transient secondary hyperparathyroidism.

J Pediatr Endocrinol Metab 2019 Dec;32(12):1399-1402

University of Miami Miller School of Medicine, Division of Pediatric Endocrinology, 1601 NW 12th Avenue, Suite 3044A, Miami, FL 33136-1015, USA, Phone: +1-305-243-5707, Fax: +1-305-243-6309.

Background Mucolipidosis II α/β (ML II) is an autosomal recessive disease associated with the abnormality of lysosomal enzyme trafficking. Case presentation We present an unusual patient with: (a) marked skeletal anomalies with secondary hyperparathyroidism; (b) serum intact parathyroid hormone level normalized by 7 weeks but abnormally elevated serum alkaline phosphate persisted; and (c) two mutations identified in the GNPTAB gene. One mutation, c.3503_3504delTC, is the most common mutation in ML II. However, the second mutation, c.2896delA, is a rare mutation for which clinical presentation has not been described previously.
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http://dx.doi.org/10.1515/jpem-2019-0162DOI Listing
December 2019

Dominant collagen XII mutations cause a distal myopathy.

Ann Clin Transl Neurol 2019 10 11;6(10):1980-1988. Epub 2019 Sep 11.

National Institutes of Health, NINDS, NNDCS, Bethesda, Maryland.

Objective: To characterize the natural history and clinical features of myopathies caused by mono-allelic, dominantly acting pathogenic variants in COL12A1.

Methods: Patients with dominant COL12A1-related myopathies were characterized by history and clinical examination, muscle imaging, and genetic analysis. Pathogenicity of the variants was assessed by immunostaining patient-derived dermal fibroblast cultures for collagen XII.

Results: Four independent families with childhood-onset weakness due to novel, dominantly acting pathogenic variants in COL12A1 were identified. Adult patients exhibited distal-predominant weakness. Three families carried dominantly acting glycine missense variants, and one family had a heterozygous, intragenic, in-frame deletion of exon 52 of COL12A1. All pathogenic variants resulted in increased intracellular retention of collagen XII in patient-derived fibroblasts as well as loss of extracellular, fibrillar collagen XII deposition. Since haploinsufficiency for COL12A1 is largely clinically asymptomatic, we designed and evaluated small interfering RNAs (siRNAs) that specifically target the mutant allele containing the exon 52 deletion. Immunostaining of the patient fibroblasts treated with the siRNA showed a near complete correction of collagen XII staining patterns.

Interpretation: This study characterizes a distal myopathy phenotype in adults with dominant COL12A1 pathogenic variants, further defining the phenotypic spectrum and natural history of COL12A1-related myopathies. This work also provides proof of concept of a precision medicine treatment approach by proposing and validating allele-specific knockdown using siRNAs specifically designed to target a patient's dominant COL12A1 disease allele.
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http://dx.doi.org/10.1002/acn3.50882DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6801183PMC
October 2019

Correction: Variants in MED12L, encoding a subunit of the Mediator kinase module, are responsible for intellectual disability associated with transcriptional defect.

Genet Med 2019 11;21(11):2663

CHU Nantes, Service de Génétique Médicale, Nantes, France.

In the Acknowledgements section of the paper the authors neglected to mention that the study was supported by a grant from the National Human Genome Research Institute (NHGRI) UM1HG007301 (S.H., M.L.T.). In addition, the award of MD was associated with the authors Michelle L. Thompson and Susan Hiatt instead of PhD. The PDF and HTML versions of the Article have been modified accordingly.
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http://dx.doi.org/10.1038/s41436-019-0590-2DOI Listing
November 2019

Variants in MED12L, encoding a subunit of the mediator kinase module, are responsible for intellectual disability associated with transcriptional defect.

Genet Med 2019 12 3;21(12):2713-2722. Epub 2019 Jun 3.

CHU Nantes, Service de Génétique Médicale, Nantes, France.

Purpose: Mediator is a multiprotein complex that allows the transfer of genetic information from DNA binding proteins to the RNA polymerase II during transcription initiation. MED12L is a subunit of the kinase module, which is one of the four subcomplexes of the mediator complex. Other subunits of the kinase module have been already implicated in intellectual disability, namely MED12, MED13L, MED13, and CDK19.

Methods: We describe an international cohort of seven affected individuals harboring variants involving MED12L identified by array CGH, exome or genome sequencing.

Results: All affected individuals presented with intellectual disability and/or developmental delay, including speech impairment. Other features included autism spectrum disorder, aggressive behavior, corpus callosum abnormality, and mild facial morphological features. Three individuals had a MED12L deletion or duplication. The other four individuals harbored single-nucleotide variants (one nonsense, one frameshift, and two splicing variants). Functional analysis confirmed a moderate and significant alteration of RNA synthesis in two individuals.

Conclusion: Overall data suggest that MED12L haploinsufficiency is responsible for intellectual disability and transcriptional defect. Our findings confirm that the integrity of this kinase module is a critical factor for neurological development.
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http://dx.doi.org/10.1038/s41436-019-0557-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7243155PMC
December 2019

De novo and inherited TCF20 pathogenic variants are associated with intellectual disability, dysmorphic features, hypotonia, and neurological impairments with similarities to Smith-Magenis syndrome.

Genome Med 2019 02 28;11(1):12. Epub 2019 Feb 28.

Centre de Génétique Humaine, Université de Franche-Comté, Besançon, France.

Background: Neurodevelopmental disorders are genetically and phenotypically heterogeneous encompassing developmental delay (DD), intellectual disability (ID), autism spectrum disorders (ASDs), structural brain abnormalities, and neurological manifestations with variants in a large number of genes (hundreds) associated. To date, a few de novo mutations potentially disrupting TCF20 function in patients with ID, ASD, and hypotonia have been reported. TCF20 encodes a transcriptional co-regulator structurally related to RAI1, the dosage-sensitive gene responsible for Smith-Magenis syndrome (deletion/haploinsufficiency) and Potocki-Lupski syndrome (duplication/triplosensitivity).

Methods: Genome-wide analyses by exome sequencing (ES) and chromosomal microarray analysis (CMA) identified individuals with heterozygous, likely damaging, loss-of-function alleles in TCF20. We implemented further molecular and clinical analyses to determine the inheritance of the pathogenic variant alleles and studied the spectrum of phenotypes.

Results: We report 25 unique inactivating single nucleotide variants/indels (1 missense, 1 canonical splice-site variant, 18 frameshift, and 5 nonsense) and 4 deletions of TCF20. The pathogenic variants were detected in 32 patients and 4 affected parents from 31 unrelated families. Among cases with available parental samples, the variants were de novo in 20 instances and inherited from 4 symptomatic parents in 5, including in one set of monozygotic twins. Two pathogenic loss-of-function variants were recurrent in unrelated families. Patients presented with a phenotype characterized by developmental delay, intellectual disability, hypotonia, variable dysmorphic features, movement disorders, and sleep disturbances.

Conclusions: TCF20 pathogenic variants are associated with a novel syndrome manifesting clinical characteristics similar to those observed in Smith-Magenis syndrome. Together with previously described cases, the clinical entity of TCF20-associated neurodevelopmental disorders (TAND) emerges from a genotype-driven perspective.
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http://dx.doi.org/10.1186/s13073-019-0623-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6393995PMC
February 2019

Clinical, radiological, and genetic characteristics of 16 patients with ACO2 gene defects: Delineation of an emerging neurometabolic syndrome.

J Inherit Metab Dis 2019 03 28;42(2):264-275. Epub 2019 Jan 28.

Rappaport Faculty of Medicine, Technion- Israel Institute of Technology, Haifa, Israel.

Mitochondrial aconitase is the second enzyme in the tricarboxylic acid (TCA) cycle catalyzing the interconversion of citrate into isocitrate and encoded by the nuclear gene ACO2. A homozygous pathogenic variant in the ACO2 gene was initially described in 2012 resulting in a novel disorder termed "infantile cerebellar retinal degeneration" (ICRD, OMIM#614559). Subsequently, additional studies reported patients with pathogenic ACO2 variants, further expanding the genetic and clinical spectrum of this disorder to include milder and later onset manifestations. Here, we report an international multicenter cohort of 16 patients (of whom 7 are newly diagnosed) with biallelic pathogenic variants in ACO2 gene. Most patients present in early infancy with severe truncal hypotonia, truncal ataxia, variable seizures, evolving microcephaly, and ophthalmological abnormalities of which the most dominant are esotropia and optic atrophy with later development of retinal dystrophy. Most patients remain nonambulatory and do no acquire any language, but a subgroup of patients share a more favorable course. Brain magnetic resonance imaging (MRI) is typically normal within the first months but global atrophy gradually develops affecting predominantly the cerebellum. Ten of our patients were homozygous to the previously reported c.336C>G founder mutation while the other six patients were all compound heterozygotes displaying 10 novel mutations of whom 2 were nonsense predicting a deleterious effect on enzyme function. Structural protein modeling predicted significant impairment in aconitase substrate binding in the additional missense mutations. This study provides the most extensive cohort of patients and further delineates the clinical, radiological, biochemical, and molecular features of ACO2 deficiency.
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http://dx.doi.org/10.1002/jimd.12022DOI Listing
March 2019

Spatially clustering de novo variants in CYFIP2, encoding the cytoplasmic FMRP interacting protein 2, cause intellectual disability and seizures.

Eur J Hum Genet 2019 05 21;27(5):747-759. Epub 2019 Jan 21.

Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia.

CYFIP2, encoding the evolutionary highly conserved cytoplasmic FMRP interacting protein 2, has previously been proposed as a candidate gene for intellectual disability and autism because of its important role linking FMRP-dependent transcription regulation and actin polymerization via the WAVE regulatory complex (WRC). Recently, de novo variants affecting the amino acid p.Arg87 of CYFIP2 were reported in four individuals with epileptic encephalopathy. We here report 12 independent patients harboring a variety of de novo variants in CYFIP2 broadening the molecular and clinical spectrum of a novel CYFIP2-related neurodevelopmental disorder. Using trio whole-exome or -genome sequencing, we identified 12 independent patients carrying a total of eight distinct de novo variants in CYFIP2 with a shared phenotype of intellectual disability, seizures, and muscular hypotonia. We detected seven different missense variants, of which two occurred recurrently (p.(Arg87Cys) and p.(Ile664Met)), and a splice donor variant in the last intron for which we showed exon skipping in the transcript. The latter is expected to escape nonsense-mediated mRNA decay resulting in a truncated protein. Despite the large spacing in the primary structure, the variants spatially cluster in the tertiary structure and are all predicted to weaken the interaction with WAVE1 or NCKAP1 of the actin polymerization regulating WRC-complex. Preliminary genotype-phenotype correlation indicates a profound phenotype in p.Arg87 substitutions and a more variable phenotype in other alterations. This study evidenced a variety of de novo variants in CYFIP2 as a novel cause of mostly severe intellectual disability with seizures and muscular hypotonia.
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http://dx.doi.org/10.1038/s41431-018-0331-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6461771PMC
May 2019

Novel fibronectin mutations and expansion of the phenotype in spondylometaphyseal dysplasia with "corner fractures".

Bone 2019 04 30;121:163-171. Epub 2018 Dec 30.

CHU Sainte Justine Research Centre and Department of Pediatrics, University of Montreal, Montreal, QC H3T 1C5, Canada. Electronic address:

Heterozygous pathogenic variants in the FN1 gene, encoding fibronectin (FN), have recently been shown to be associated with a skeletal disorder in some individuals affected by spondylometaphyseal dysplasia with "corner fractures" (SMD-CF). The most striking feature characterizing SMD-CF is irregularly shaped metaphyses giving the appearance of "corner fractures". An array of secondary features, including developmental coxa vara, ovoid vertebral bodies and severe scoliosis, may also be present. FN is an important extracellular matrix component for bone and cartilage development. Here we report five patients affected by this subtype of SMD-CF caused by five novel FN1 missense mutations: p.Cys123Tyr, p.Cys169Tyr, p.Cys213Tyr, p.Cys231Trp and p.Cys258Tyr. All individuals shared a substitution of a cysteine residue, disrupting disulfide bonds in the FN type-I assembly domains located in the N-terminal assembly region. The abnormal metaphyseal ossification and "corner fracture" appearances were the most remarkable clinical feature in these patients. In addition, generalized skeletal fragility with low-trauma bilateral femoral fractures was identified in one patient. Interestingly, the distal femoral changes in this patient healed with skeletal maturation. Our report expands the phenotypic and genetic spectrum of the FN1-related SMD-CF and emphasizes the importance of FN in bone formation and possibly also in the maintenance of bone strength.
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http://dx.doi.org/10.1016/j.bone.2018.12.020DOI Listing
April 2019

The first case of deafness-dystonia syndrome due to compound heterozygous variants in .

Clin Case Rep 2018 Sep 26;6(9):1815-1817. Epub 2018 Jul 26.

Section of Genetics Department of Pediatrics University of Oklahoma Health Sciences Center Oklahoma City Oklahoma.

We report the second known family affected by deafness-dystonia syndrome associated with loss of function of . Our patient is compound heterozygous for pathogenic variants, while affected siblings in the first report were homozygous. This case provides evidence that this novel genetic disorder is associated with autosomal recessive inheritance.
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http://dx.doi.org/10.1002/ccr3.1719DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6132111PMC
September 2018

Site-1 protease deficiency causes human skeletal dysplasia due to defective inter-organelle protein trafficking.

JCI Insight 2018 07 26;3(14). Epub 2018 Jul 26.

Cardiovascular Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA.

Site-1 protease (S1P), encoded by MBTPS1, is a serine protease in the Golgi. S1P regulates lipogenesis, endoplasmic reticulum (ER) function, and lysosome biogenesis in mice and in cultured cells. However, how S1P differentially regulates these diverse functions in humans has been unclear. In addition, no human disease with S1P deficiency has been identified. Here, we report a pediatric patient with an amorphic and a severely hypomorphic mutation in MBTPS1. The unique combination of these mutations results in a frequency of functional MBTPS1 transcripts of approximately 1%, a finding that is associated with skeletal dysplasia and elevated blood lysosomal enzymes. We found that the residually expressed S1P is sufficient for lipid homeostasis but not for ER and lysosomal functions, especially in chondrocytes. The defective S1P function specifically impairs activation of the ER stress transducer BBF2H7, leading to ER retention of collagen in chondrocytes. S1P deficiency also causes abnormal secretion of lysosomal enzymes due to partial impairment of mannose-6-phosphate-dependent delivery to lysosomes. Collectively, these abnormalities lead to apoptosis of chondrocytes and lysosomal enzyme-mediated degradation of the bone matrix. Correction of an MBTPS1 variant or reduction of ER stress mitigated collagen-trafficking defects. These results define a new congenital human skeletal disorder and, more importantly, reveal that S1P is particularly required for skeletal development in humans. Our findings may also lead to new therapies for other genetic skeletal diseases, as ER dysfunction is common in these disorders.
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http://dx.doi.org/10.1172/jci.insight.121596DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6124414PMC
July 2018

βIV Spectrinopathies Cause Profound Intellectual Disability, Congenital Hypotonia, and Motor Axonal Neuropathy.

Am J Hum Genet 2018 06 31;102(6):1158-1168. Epub 2018 May 31.

Department of Neuroscience and Integrative Molecular and Biomedical Sciences Graduate Program, Baylor College of Medicine, Houston, TX 77030, USA. Electronic address:

βIV spectrin links ankyrinG (AnkG) and clustered ion channels at axon initial segments (AISs) and nodes of Ranvier to the axonal cytoskeleton. Here, we report bi-allelic pathogenic SPTBN4 variants (three homozygous and two compound heterozygous) that cause a severe neurological syndrome that includes congenital hypotonia, intellectual disability, and motor axonal and auditory neuropathy. We introduced these variants into βIV spectrin, expressed these in neurons, and found that 5/7 were loss-of-function variants disrupting AIS localization or abolishing phosphoinositide binding. Nerve biopsies from an individual with a loss-of-function variant had reduced nodal Na channels and no nodal KCNQ2 K channels. Modeling the disease in mice revealed that although ankyrinR (AnkR) and βI spectrin can cluster Na channels and partially compensate for the loss of AnkG and βIV spectrin at nodes of Ranvier, AnkR and βI spectrin cannot cluster KCNQ2- and KCNQ3-subunit-containing K channels. Our findings define a class of spectrinopathies and reveal the molecular pathologies causing nervous-system dysfunction.
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http://dx.doi.org/10.1016/j.ajhg.2018.04.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5992132PMC
June 2018

A novel NAA10 variant with impaired acetyltransferase activity causes developmental delay, intellectual disability, and hypertrophic cardiomyopathy.

Eur J Hum Genet 2018 09 10;26(9):1294-1305. Epub 2018 May 10.

Department of Biological Sciences, University of Bergen, 5020, Bergen, Norway.

The NAA10-NAA15 complex (NatA) is an N-terminal acetyltransferase that catalyzes N-terminal acetylation of ~40% of all human proteins. N-terminal acetylation has several different roles in the cell, including altering protein stability and degradation, protein localization and protein-protein interactions. In recent years several X-linked NAA10 variants have been associated with genetic disorders. We have identified a previously undescribed NAA10 c.215T>C p.(Ile72Thr) variant in three boys from two unrelated families with a milder phenotypic spectrum in comparison to most of the previously described patients with NAA10 variants. These boys have development delay, intellectual disability, and cardiac abnormalities as overlapping phenotypes. Functional studies reveal that NAA10 Ile72Thr is destabilized, while binding to NAA15 most likely is intact. Surprisingly, the NatA activity of NAA10 Ile72Thr appears normal while its monomeric activity is decreased. This study further broadens the phenotypic spectrum associated with NAA10 deficiency, and adds to the evidence that genotype-phenotype correlations for NAA10 variants are much more complex than initially anticipated.
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http://dx.doi.org/10.1038/s41431-018-0136-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6117304PMC
September 2018

A Recurrent De Novo PACS2 Heterozygous Missense Variant Causes Neonatal-Onset Developmental Epileptic Encephalopathy, Facial Dysmorphism, and Cerebellar Dysgenesis.

Am J Hum Genet 2018 05 12;102(5):995-1007. Epub 2018 Apr 12.

University of Groningen, University Medical Center Groningen, Department of Genetics, 9700 RB Groningen, the Netherlands.

Developmental and epileptic encephalopathies (DEEs) represent a large clinical and genetic heterogeneous group of neurodevelopmental diseases. The identification of pathogenic genetic variants in DEEs remains crucial for deciphering this complex group and for accurately caring for affected individuals (clinical diagnosis, genetic counseling, impacting medical, precision therapy, clinical trials, etc.). Whole-exome sequencing and intensive data sharing identified a recurrent de novo PACS2 heterozygous missense variant in 14 unrelated individuals. Their phenotype was characterized by epilepsy, global developmental delay with or without autism, common cerebellar dysgenesis, and facial dysmorphism. Mixed focal and generalized epilepsy occurred in the neonatal period, controlled with difficulty in the first year, but many improved in early childhood. PACS2 is an important PACS1 paralog and encodes a multifunctional sorting protein involved in nuclear gene expression and pathway traffic regulation. Both proteins harbor cargo(furin)-binding regions (FBRs) that bind cargo proteins, sorting adaptors, and cellular kinase. Compared to the defined PACS1 recurrent variant series, individuals with PACS2 variant have more consistently neonatal/early-infantile-onset epilepsy that can be challenging to control. Cerebellar abnormalities may be similar but PACS2 individuals exhibit a pattern of clear dysgenesis ranging from mild to severe. Functional studies demonstrated that the PACS2 recurrent variant reduces the ability of the predicted autoregulatory domain to modulate the interaction between the PACS2 FBR and client proteins, which may disturb cellular function. These findings support the causality of this recurrent de novo PACS2 heterozygous missense in DEEs with facial dysmorphim and cerebellar dysgenesis.
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http://dx.doi.org/10.1016/j.ajhg.2018.03.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5986694PMC
May 2018

High Rate of Recurrent De Novo Mutations in Developmental and Epileptic Encephalopathies.

Am J Hum Genet 2017 Nov;101(5):664-685

Manchester Centre for Genomic Medicine, St. Mary's Hospital, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester M13 9WL, UK.

Developmental and epileptic encephalopathy (DEE) is a group of conditions characterized by the co-occurrence of epilepsy and intellectual disability (ID), typically with developmental plateauing or regression associated with frequent epileptiform activity. The cause of DEE remains unknown in the majority of cases. We performed whole-genome sequencing (WGS) in 197 individuals with unexplained DEE and pharmaco-resistant seizures and in their unaffected parents. We focused our attention on de novo mutations (DNMs) and identified candidate genes containing such variants. We sought to identify additional subjects with DNMs in these genes by performing targeted sequencing in another series of individuals with DEE and by mining various sequencing datasets. We also performed meta-analyses to document enrichment of DNMs in candidate genes by leveraging our WGS dataset with those of several DEE and ID series. By combining these strategies, we were able to provide a causal link between DEE and the following genes: NTRK2, GABRB2, CLTC, DHDDS, NUS1, RAB11A, GABBR2, and SNAP25. Overall, we established a molecular diagnosis in 63/197 (32%) individuals in our WGS series. The main cause of DEE in these individuals was de novo point mutations (53/63 solved cases), followed by inherited mutations (6/63 solved cases) and de novo CNVs (4/63 solved cases). De novo missense variants explained a larger proportion of individuals in our series than in other series that were primarily ascertained because of ID. Moreover, these DNMs were more frequently recurrent than those identified in ID series. These observations indicate that the genetic landscape of DEE might be different from that of ID without epilepsy.
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http://dx.doi.org/10.1016/j.ajhg.2017.09.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5673604PMC
November 2017

Inferred inheritance of MorbidMap genes without OMIM clinical synopsis.

Genet Med 2018 04 24;20(4):470-473. Epub 2017 Aug 24.

Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA.

PurposeThe Genomic Oligoarray and SNP Array Evaluation Tool 3.0 matches candidate genes within regions of homozygosity with a patient's phenotype, by mining OMIM for gene entries that contain a Clinical Synopsis. However, the tool cannot identify genes/disorders whose OMIM entries lack a descriptor of the mode of (Mendelian) inheritance. This study aimed to improve the tool's diagnostic power by building a database of autosomal recessive diseases not diagnosable through OMIM.MethodsWe extracted a list of all genes in OMIM that produce disease phenotypes but lack Clinical Synopses or other statements of mode of inheritance. We then searched PubMed for literature regarding each gene in order to infer its inheritance pattern.ResultsWe analyzed 1,392 genes. Disorders associated with 372 genes were annotated as recessive and 430 as dominant. Autosomal genes were ranked from 1 to 3, with 3 indicating the strongest evidence behind the inferred mode of inheritance. Of 834 autosomal genes, 158 were ranked as 1, 228 as 2, and 448 as 3.ConclusionThe 372 genes associated with recessive disorders will be contributed to the SNP array tool, and the entire database to OMIM. We anticipate that these findings will be useful in rare disease diagnostics.
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http://dx.doi.org/10.1038/gim.2017.131DOI Listing
April 2018

Mutations in KEOPS-complex genes cause nephrotic syndrome with primary microcephaly.

Nat Genet 2017 Oct 14;49(10):1529-1538. Epub 2017 Aug 14.

Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium.

Galloway-Mowat syndrome (GAMOS) is an autosomal-recessive disease characterized by the combination of early-onset nephrotic syndrome (SRNS) and microcephaly with brain anomalies. Here we identified recessive mutations in OSGEP, TP53RK, TPRKB, and LAGE3, genes encoding the four subunits of the KEOPS complex, in 37 individuals from 32 families with GAMOS. CRISPR-Cas9 knockout in zebrafish and mice recapitulated the human phenotype of primary microcephaly and resulted in early lethality. Knockdown of OSGEP, TP53RK, or TPRKB inhibited cell proliferation, which human mutations did not rescue. Furthermore, knockdown of these genes impaired protein translation, caused endoplasmic reticulum stress, activated DNA-damage-response signaling, and ultimately induced apoptosis. Knockdown of OSGEP or TP53RK induced defects in the actin cytoskeleton and decreased the migration rate of human podocytes, an established intermediate phenotype of SRNS. We thus identified four new monogenic causes of GAMOS, describe a link between KEOPS function and human disease, and delineate potential pathogenic mechanisms.
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http://dx.doi.org/10.1038/ng.3933DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5819591PMC
October 2017
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