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2.
J Hum Genet ; 64(12): 1173-1186, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31530938

RESUMO

Coffin-Siris syndrome (CSS, MIM#135900) is a congenital disorder characterized by coarse facial features, intellectual disability, and hypoplasia of the fifth digit and nails. Pathogenic variants for CSS have been found in genes encoding proteins in the BAF (BRG1-associated factor) chromatin-remodeling complex. To date, more than 150 CSS patients with pathogenic variants in nine BAF-related genes have been reported. We previously reported 71 patients of whom 39 had pathogenic variants. Since then, we have recruited an additional 182 CSS-suspected patients. We performed comprehensive genetic analysis on these 182 patients and on the previously unresolved 32 patients, targeting pathogenic single nucleotide variants, short insertions/deletions and copy number variations (CNVs). We confirmed 78 pathogenic variations in 78 patients. Pathogenic variations in ARID1B, SMARCB1, SMARCA4, ARID1A, SOX11, SMARCE1, and PHF6 were identified in 48, 8, 7, 6, 4, 1, and 1 patients, respectively. In addition, we found three CNVs including SMARCA2. Of particular note, we found a partial deletion of SMARCB1 in one CSS patient and we thoroughly investigated the resulting abnormal transcripts.

4.
Neurology ; 93(3): e237-e251, 2019 Jul 16.
Artigo em Inglês | MEDLINE | ID: mdl-31197031

RESUMO

OBJECTIVE: Intensive genetic analysis was performed to reveal comprehensive molecular insights into hypothalamic hamartoma (HH). METHODS: Thirty-eight individuals with HH were investigated by whole exome sequencing, target capture-based deep sequencing, or single nucleotide polymorphism (SNP) array using DNA extracted from blood leukocytes or HH samples. RESULTS: We identified a germline variant of KIAA0556, which encodes a ciliary protein, and 2 somatic variants of PTPN11, which forms part of the RAS/mitogen-activated protein kinase (MAPK) pathway, as well as variants in known genes associated with HH. An SNP array identified (among 3 patients) one germline copy-neutral loss of heterozygosity (cnLOH) at 6p22.3-p21.31 and 2 somatic cnLOH; one at 11q12.2-q25 that included DYNC2H1, which encodes a ciliary motor protein, and the other at 17p13.3-p11.2. A germline heterozygous variant and an identical somatic variant of DYNC2H1 arising from cnLOH at 11q12.2-q25 were confirmed in one patient (whose HH tissue, therefore, contains biallelic variants of DYNC2H1). Furthermore, a combination of a germline and a somatic DYNC2H1 variant was detected in another patient. CONCLUSIONS: Overall, our cohort identified germline/somatic alterations in 34% (13/38) of patients with HH. Disruption of the Shh signaling pathway associated with cilia or the RAS/MAPK pathway may lead to the development of HH.

6.
Intern Med ; 58(18): 2715-2719, 2019 Sep 15.
Artigo em Inglês | MEDLINE | ID: mdl-31178479

RESUMO

A 24-year-old Japanese man exhibited slowly progressive gait disturbance from childhood to young adulthood. Physical and physiological examinations showed the involvement of both upper and lower motor neurons, fulfilling the diagnostic criteria for amyotrophic lateral sclerosis (ALS). Mild cognitive impairment and subclinical sensory involvement were also observed. A genetic analysis revealed novel compound heterozygous mutations, c.767C>T (p.Thr256Ile) and c.800A>G (p.Asp267Gly), in the vaccinia-related kinase 1 gene (VRK1). This is the first report of a Japanese patient with a motor neuron disease phenotype caused by VRK1 mutations. This diagnosis should be considered in atypical cases of juvenile-onset and slowly progressive types of motor neuron disease.

7.
Clin Genet ; 95(6): 713-717, 2019 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-30847897

RESUMO

Desbuquois dysplasia (DBQD) is an autosomal recessive heterogeneous disorder characterized by joint laxity and skeletal changes, including a distinctive monkey-wrench appearance of the femora, advanced carpal ossification, and abnormal patterning of the preaxial digits. Two genes for DBQD (CANT1 encoding calcium-activated nucleotidase-1 and XYLT1 encoding xylosyltransferase-1) have been reported. We propose a novel gene for neonatal short limb dysplasia resembling DBQD, based on the phenotype and genotype of two affected siblings. The affected boy and girl died in early infancy and shortly after birth, respectively. The clinical hallmarks included mid-face hypoplasia, thoracic hypoplasia with respiratory failure, very short stature (approximately -7 SD of birth length) with mesomelic shortening of the limbs, and multiple dislocations of the large joints. Radiological examinations showed prominent lesser trochanter, flared metaphyses of the long bones, and joint dislocations. The affected boy had preaxial digital hypoplasia, and the affected girl showed overlapping and syndactyly of the preaxial digits. Molecular analyses of the girl showed compound heterozygous variants in FAM20B (NM_014864: c.174_178delTACCT p.T59Afs*19/c.1038delG p.N347Mfs*4). FAM20B encodes glycosaminoglycan xylosylkinase, which acts downstream of xylosyltransferase-1. Given the fact that FAM20B deficiency causes skeletal phenotypes in mice and zebrafish, these variants are highly probable to be pathogenic.

8.
Brain Dev ; 41(6): 538-541, 2019 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-30795918

RESUMO

PPM1D truncating mutations in the last and penultimate exons of the gene have been associated with intellectual disability (ID) syndrome. Only 15 affected patients to-date have been reported with mild-to-severe ID, autistic behavior, anxiety and dysmorphic features. Here, we describe the clinical characteristics and underlying genetics of two unrelated girls with moderate developmental delay and dysmorphic features associated with novel mutations in PPM1D exon 5. The dysmorphic features demonstrated by these two patients are consistent with previously reported patients, including broad forehead, thin upper lip, brachydactyly, and hypoplastic nails. We identified a de novo PPM1D mutation in exon 5 of each patient (c.1250_1251insACCA p.V419Tfs*16 and c.1256_1257insCAAG p.S421Qfs*14) by panel sequencing for 4,813 disease-related genes. Both patients also had frameshift mutations (at different positions) that resulted in the same estimated termination codon at 434. These additional reports add to the growing literature on PPM1D-associated ID syndrome and help delineate the clinical phenotype and genetic basis.


Assuntos
Deficiência Intelectual/genética , Proteína Fosfatase 2C/genética , Proteína Fosfatase 2C/fisiologia , Criança , Pré-Escolar , Deficiências do Desenvolvimento/genética , Éxons/genética , Feminino , Mutação da Fase de Leitura/genética , Genótipo , Humanos , Deficiência Intelectual/metabolismo , Mutação/genética , Fenótipo , Sequenciamento Completo do Exoma/métodos
9.
Ann Neurol ; 2018 Nov 14.
Artigo em Inglês | MEDLINE | ID: mdl-30427554

RESUMO

OBJECTIVE: Galloway-Mowat syndrome (GAMOS) is a neural and renal disorder, characterized by microcephaly, brain anomalies, and early-onset nephrotic syndrome. Biallelic mutations in WDR73 and the four subunit genes of the KEOPS complex are reported to cause GAMOS. Furthermore, an identical homozygous NUP107 (nucleoporin 107 kDa) mutation was identified in four GAMOS-like families, although biallelic NUP107 mutations were originally identified in steroid-resistant nephrotic syndrome. NUP107 and NUP133 (nucleoporin 133 kDa) are interacting subunits of the nuclear pore complex in the nuclear envelope during interphase, and these proteins are also involved in centrosome positioning and spindle assembly during mitosis. METHODS: Linkage analysis and whole exome sequencing were performed in a previously reported GAMOS family with brain atrophy and steroid-resistant nephrotic syndrome. RESULTS: We identified a homozygous NUP133 mutation, c.3335-11T>A, which results in the insertion of 9 bp of intronic sequence between exons 25 and 26 in the mutant transcript. NUP133 and NUP107 interaction was impaired by the NUP133 mutation based on an immunoprecipitation assay. Importantly, focal cortical dysplasia type IIa was recognized in the brain of an autopsied patient and focal segmental glomerulosclerosis was confirmed in the kidneys of the three examined patients. A nup133-knockdown zebrafish model exhibited microcephaly, fewer neuronal cells, underdeveloped glomeruli, and fusion of the foot processes of the podocytes, which mimicked human GAMOS features. nup133 morphants could be rescued by human wildtype NUP133 mRNA but not by mutant mRNA. INTERPRETATION: These data indicate that the biallelic NUP133 loss-of-function mutation causes GAMOS. This article is protected by copyright. All rights reserved.

10.
Genet Med ; 2018 Nov 23.
Artigo em Inglês | MEDLINE | ID: mdl-30467404

RESUMO

PURPOSE: The diagnostic rate for Mendelian diseases by exome sequencing (ES) is typically 20-40%. The low rate is partly because ES misses deep-intronic or synonymous variants leading to aberrant splicing. In this study, we aimed to apply RNA sequencing (RNA-seq) to efficiently detect the aberrant splicings and their related variants. METHODS: Aberrant splicing in biopsied muscles from six nemaline myopathy (NM) cases unresolved by ES were analyzed with RNA-seq. Variants related to detected aberrant splicing events were analyzed with Sanger sequencing. Detected variants were screened in NM patients unresolved by ES. RESULTS: We identified a novel deep-intronic NEB pathogenic variant, c.1569+339A>G in one case, and another novel synonymous NEB pathogenic variant, c.24684G>C (p.Ser8228Ser) in three cases. The c.24684G>C variant was observed to be the most frequent among all NEB pathogenic variants in normal Japanese populations with a frequency of 1 in 178 (20 alleles in 3552 individuals), but was previously unrecognized. Expanded screening of the variant identified it in a further four previously unsolved nemaline myopathy cases. CONCLUSION: These results indicated that RNA-seq may be able to solve a large proportion of previously undiagnosed muscle diseases.

11.
Hum Genome Var ; 5: 20, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-30062040

RESUMO

SCN2A mutations are primarily associated with a variety of epilepsy syndromes. Recently, SCN2A has been reported as a gene responsible for nonsyndromic intellectual disability or autism spectrum disorders. Here, we present a case of a 12-year-old girl with nonsyndromic intellectual disability who exhibited a heterozygous de novo missense mutation in SCN2A. She developed seizures during the course of illness. This case suggests that the phenotype of patients with heterozygous SCN2A mutations can be variable.

12.
Hum Genome Var ; 5: 11, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-29899996

RESUMO

Epidermal growth factor receptor (EGFR), a receptor that recognizes epidermal growth factor, is a very important regulator of cell proliferation and differentiation. To date, three cases of severe ectodermal dysplasia were reported to be caused by an inherited germline homozygous loss-of-function missense mutation of EGFR. This is the first report of a patient with biallelic compound heterozygous mutations in EGFR.

13.
Hum Genome Var ; 5: 4, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-29760938

RESUMO

Porencephaly and schizencephaly are congenital brain disorders that can be caused by COL4A1 mutations, though the underlying mechanism and developmental processes are poorly understood. Here, we report a patient with schizencephaly, detected by fetal ultrasonography and fetal magnetic resonance imaging, with a de novo novel mutation in COL4A1 (c.2645_2646delinsAA, p.Gly882Glu). Our results suggest that the onset of damage that potentially results in schizencephaly occurs mid-pregnancy.

14.
Hum Genome Var ; 5: 18011, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-29619237

RESUMO

We describe an 8-year-old Japanese boy with a de novo recurrent missense mutation in CSNK2A1, c.593A>G, that is causative of Okur-Chung neurodevelopmental syndrome. He exhibited distinctive facial features, severe growth retardation with relative macrocephaly, and friendly, hyperactive behavior. His dysmorphic features might suggest a congenital histone modification defect syndrome, such as Kleefstra, Coffin-Siris, or Rubinstein-Taybi syndromes, which are indicative of functional interactions between the casein kinase II, alpha 1 gene and histone modification factors.

15.
Ann Neurol ; 83(4): 794-806, 2018 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-29534297

RESUMO

OBJECTIVE: The cytoplasmic fragile X mental retardation 1 interacting proteins 2 (CYFIP2) is a component of the WASP-family verprolin-homologous protein (WAVE) regulatory complex, which is involved in actin dynamics. An obvious association of CYFIP2 variants with human neurological disorders has never been reported. Here, we identified de novo hotspot CYFIP2 variants in neurodevelopmental disorders and explore the possible involvement of the CYFIP2 mutants in the WAVE signaling pathway. METHODS: We performed trio-based whole-exome sequencing (WES) in 210 families and case-only WES in 489 individuals with epileptic encephalopathies. The functional effect of CYFIP2 variants on WAVE signaling was evaluated by computational structural analysis and in vitro transfection experiments. RESULTS: We identified three de novo CYFIP2 variants at the Arg87 residue in 4 unrelated individuals with early-onset epileptic encephalopathy. Structural analysis indicated that the Arg87 residue is buried at an interface between CYFIP2 and WAVE1, and the Arg87 variant may disrupt hydrogen bonding, leading to structural instability and aberrant activation of the WAVE regulatory complex. All mutant CYFIP2 showed comparatively weaker interactions to the VCA domain than wild-type CYFIP2. Immunofluorescence revealed that ectopic speckled accumulation of actin and CYFIP2 was significantly increased in cells transfected with mutant CYFIP2. INTERPRETATION: Our findings suggest that de novo Arg87 variants in CYFIP2 have gain-of-function effects on the WAVE signaling pathway and are associated with severe neurological disorders. Ann Neurol 2018;83:794-806.

16.
J Hum Genet ; 63(4): 417-423, 2018 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-29403087

RESUMO

Autosomal recessive cerebellar ataxias (ARCAs) are clinically and genetically heterogeneous neurological disorders. Through whole-exome sequencing of Japanese ARCA patients, we identified three index patients from unrelated families who had biallelic mutations in ERCC4. ERCC4 mutations have been known to cause xeroderma pigmentosum complementation group F (XP-F), Cockayne syndrome, and Fanconi anemia phenotypes. All of the patients described here showed very slowly progressive cerebellar ataxia and cognitive decline with choreiform involuntary movement, with young adolescent or midlife onset. Brain MRI demonstrated atrophy that included the cerebellum and brainstem. Of note, cutaneous symptoms were very mild: there was normal to very mild pigmentation of exposed skin areas and/or an equivocal history of pathological sunburn. However, an unscheduled DNA synthesis assay of fibroblasts from the patient revealed impairment of nucleotide excision repair. A similar phenotype was very recently recognized through genetic analysis of Caucasian cerebellar ataxia patients. Our results confirm that biallelic ERCC4 mutations cause a cerebellar ataxia-dominant phenotype with mild cutaneous symptoms, possibly accounting for a high proportion of the genetic causes of ARCA in Japan, where XP-F is prevalent.


Assuntos
Ataxia Cerebelar/diagnóstico , Ataxia Cerebelar/genética , Proteínas de Ligação a DNA/genética , Genes Dominantes , Mutação , Fenótipo , Adulto , Idade de Início , Idoso , Alelos , Sequência de Aminoácidos , Substituição de Aminoácidos , Encéfalo/anormalidades , Encéfalo/diagnóstico por imagem , Análise Mutacional de DNA , Feminino , Estudos de Associação Genética , Genótipo , Humanos , Imagem por Ressonância Magnética , Masculino , Linhagem
17.
Congenit Anom (Kyoto) ; 58(6): 188-190, 2018 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-29381230

RESUMO

We describe a novel de novo heterozygous variant in SYNGAP1 (c.1741C>T, p.R581W), identified through targeted resequencing in an 8-year-old boy with intellectual disability, autism spectrum disorder, distinctive dysmorphic features, and no seizures. Our data strongly suggest that the SYNGAP1 variant is causative of intellectual disability in this patient.

18.
Cell Rep ; 22(3): 734-747, 2018 Jan 16.
Artigo em Inglês | MEDLINE | ID: mdl-29346770

RESUMO

Recent studies have established important roles of de novo mutations (DNMs) in autism spectrum disorders (ASDs). Here, we analyze DNMs in 262 ASD probands of Japanese origin and confirm the "de novo paradigm" of ASDs across ethnicities. Based on this consistency, we combine the lists of damaging DNMs in our and published ASD cohorts (total number of trios, 4,244) and perform integrative bioinformatics analyses. Besides replicating the findings of previous studies, our analyses highlight ATP-binding genes and fetal cerebellar/striatal circuits. Analysis of individual genes identified 61 genes enriched for damaging DNMs, including ten genes for which our dataset now contributes to statistical significance. Screening of compounds altering the expression of genes hit by damaging DNMs reveals a global downregulating effect of valproic acid, a known risk factor for ASDs, whereas cardiac glycosides upregulate these genes. Collectively, our integrative approach provides deeper biological and potential medical insights into ASDs.

19.
Congenit Anom (Kyoto) ; 58(3): 105-107, 2018 May.
Artigo em Inglês | MEDLINE | ID: mdl-28787104

RESUMO

Coffin-Siris syndrome (CSS) is characterized by growth deficiency, intellectual disability, microcephaly, dysmorphic features, and hypoplastic nails of the fifth fingers and/or toes. Variants in the genes encoding subunits of the BAF complex as well as in SOX11 encoding the transcriptional factor under the control of BAF complex are associated with CSS. We report a new patient with a novel SOX11 mutation. He showed the CSS phenotype and coarctation of the aorta. Sox11 is known to be associated with cardiac outflow development in mouse studies. Therefore, cardiac anomalies might be an important complication in patients with SOX11 mutations.


Assuntos
Anormalidades Múltiplas/genética , Coartação Aórtica/genética , Face/anormalidades , Deformidades Congênitas da Mão/genética , Deficiência Intelectual/genética , Micrognatismo/genética , Mutação , Pescoço/anormalidades , Fatores de Transcrição SOXC/genética , Anormalidades Múltiplas/diagnóstico por imagem , Anormalidades Múltiplas/patologia , Coartação Aórtica/diagnóstico por imagem , Coartação Aórtica/patologia , Pré-Escolar , Angiografia por Tomografia Computadorizada , Ecocardiografia , Face/diagnóstico por imagem , Face/patologia , Expressão Gênica , Deformidades Congênitas da Mão/diagnóstico por imagem , Deformidades Congênitas da Mão/patologia , Humanos , Deficiência Intelectual/diagnóstico por imagem , Deficiência Intelectual/patologia , Masculino , Micrognatismo/diagnóstico por imagem , Micrognatismo/patologia , Pescoço/diagnóstico por imagem , Pescoço/patologia , Fenótipo
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