SLC25A22 is a novel gene for migrating partial seizures in infancy (original) (raw)
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SLC25A22is a novel gene for migrating partial seizures in infancy
Annals of Neurology, 2013
Objective-To identify a genetic cause for migrating partial seizures in infancy (MPSI). Methods-We characterized a consanguineous pedigree with MPSI and obtained DNA from affected and unaffected family members. We analyzed single nucleotide polymorphism (SNP) 500K data to identify regions with evidence for linkage. We performed whole exome sequencing and analyzed homozygous variants in regions of linkage to identify a candidate gene and performed functional studies of the candidate gene SLC25A22. Results-In a consanguineous pedigree with two individuals with MPSI, we identified two regions of linkage, chromosome 4p16.1-p16.3 and chromosome 11p15.4-pter. Using whole exome sequencing, we identified 8 novel homozygous variants in genes in these regions. Only one variant, SLC25A22 c.G328C, results in a change of a highly conserved amino acid (p.G110R) and was not present in control samples. SLC25A22 encodes a glutamate transporter with strong expression in the developing brain. We show that the specific G110R mutation, located in a transmembraine domain of the protein, disrupts mitochondrial glutamate transport. Interpretation-We have shown that MPSI can be inherited and have identified a novel homozygous mutation in SLC25A22 in the affected individuals. Our data strongly suggest that SLC25A22 is responsible for MPSI, a severe condition with few known etiologies. We have demonstrated that a combination of linkage analysis and whole exome sequencing can be used for disease gene discovery. Finally, as SLC25A22 had been implicated in the distinct syndrome neonatal epilepsy with suppression bursts on EEG, we have expanded the phenotypic spectrum associated with SLC25A22.
Mapping of Genes Involved in Neurological Disorders in Pakistani Families
2015
List of Tables Table No. Titles Page No. 1.1 Shows the various class of Neurological Disorders 1.2 Genes involved in non-syndromic X-linked mental retardation 1.3 The known loci of NS-ARID 3.1 Composition of Buffers and Solutions for DNA Extraction 3.2 The amount of TKM2 required blood samples 3.3 The ratio of 10% SDS required for each blood sample 3.4 The ratio of NaCl per volume of blood sample 3.5 The sequence of FMR1 gene primers and product size 3.6 Primer sequence of whole transcript of DCPS gene 3.7 The chemical preparation of ligation mixture 3.8 The composition of PCR reaction mixture 3.9 Sequence of the plasmid specific primers and product size 3.10 Master mixture for colony PCR 3.11 Primer Sequence for Full Length DCPS gene 3.12 The composition reaction mixture for restriction endonculeases Activity 3.13 Chemical composition of ligation mixture and volume required for reaction 3.14 Sequence of primers for generation of labeled RNA 4.1 The sex, ages and head circumference of affected individuals of Family A 4.2 Homozygous regions flanking between SNPs in Family A ii 4.3 The age, sex, head circumference and height of the affected individuals of Family B. 90 4.4 Amino Acid Profiling of affected individual (II:04) 93 4.5 Amino Acid Profiling of affected individual (III:04) 94 4.6 The sex, ages and head circumference of affected individuals of Family C. 4.7 List of genes on1q25.3-q31.1 locus with OMIM ID and function. 4.8 All HBD regions (hg19) determined by ChAS analysis for MM1-4,7,8,11,12, using filter cutoff of >100 markers and >1Mb. Homozygous coding variants from DNASTAR NGen analysis and ANNOVAR analysis of WES data for MM1-7 are shown, excluding synonymous and known SNPs. Integrated Genome Viewer (IGV) was used to confirm the variant. For amino acid substitutions we used Condel-an integrated analysis that uses prediction from five different algorithms, including PolyPhen2, SIFT, and Mutation Assessor (Gonzalez-Perez & Lopez-Bigas, 2011). iv show deceased ones. 4.2 Facial images, with front and side pose of patients of Family A. The facial photographs of affected individuals do not show any facial dysmorphism. The III:8 individual of this family was phenotypically quite different from others. 4.3 MRI images of affected individual V:3 showing lateral and top and dorso-lateral of view of brain. Overall structure of brain appears normal. 4.4 Whole genome homozygosity (WGH) picture of family A with significant homozygous peaks (indicated by red lines) at 01, 03, 05, 11, 14, 15 and 17 and heterozygous peaks are represented by black lines. 4.5 (A) The dChip analysed SNP data on chromosome 03, (B) Chromsome 05, (C) Chromosome 11, (D) Chromsome 14, (E) Chromsome 16 and (F) chromosome 17. Each individual was represented in columns (III:2 and V:3 are affected and III:3 is normal). Blue colour depicts homozygous region and yellow colour shows heterozygous region. 4.6 UCSC genome browser view of the 11q25.1-q25 locus. 4.7 The whole exome sequencing of Family A showing the G> A transition. The snapshot was obtained from IGV tool. 4.8 The DNA sequence chromatogram of DcpS gene of Family A. v A) The sequence showing the G>A mutation in affected individuals (III-and V-5). B) The sequence shows the heterozygous/carrier individuals of Family A. C). The sequence of normal individual. The Green colour = Adenine, Red colour = Thymine, Blue colour = Cytosine, Black colour = Guanine. 4.9 A) The affected individual (V:7) carries a heterozygous mutation on exon 6 of DcpS gene where C>T. B) The mutant allele was sequenced from the cDNA of V:7 showing the presence of C>T change. C) The chromatogram shows the individual (IV-6) is heterozygous and carrier. D) The individual IV:5 was normal Green colour = Adenine, Red colour = Thymine, Blue colour = Cytosine, Black colour = Guanine. 4.10 The sequence of full transcript (cDNA) of DcpS gene were BLAT in UCSC genome browser showing G>A transition in mutant transcript. 4.11 Schematic representation of splice site mutation in Family A. A change in splice donor usage at exon 4/intron 4 for the splice variant allele resulting in splicing of transcript 45 nucleotide down in intronic region. The resulting mRNA carries an additional 45 nucleotides. 4.12 Full transcript alignment of normal (norm) and mutant (alta) with 45 nucleotide insertion with ClustaLW2 an online tool. vi 4.13 Sequence alignment of amino acids of normal and mutant with 15 amino acid insertions. 4.14 3D-protein modelling of wild type and mutant with 15 amino acid insertion was generated by using SWISS MODEL workplace and visualized with PyMol Molecular Graphics System (http://www.pymol.org/). The location of the inserted sequence (between residues 212 to 228 mutant protein) is indicated with a yellow arrow. 4.15 Full transcript sequencing result showing 947C>T transition of affected individual (V:7). 4.16 DcpS catalyzes the hydrolysis of cap structure. Decapping assays were carried out with the indicated amounts of DcpS at the top of picture. 32P-labeled methylated cap structure (m7Gpppp) is used as substrate where red colour "p" in m 7 GpppG represented labelled phosphate and m7Gp as product of DcpS catalyzed reaction. The quantitation for the decapping efficiency of each protein is presented as the percentage decapping using ImageQuant 5.2 software at the bottom of picture. 4.17 Decapping assays of wild type and mutant DcpS from whole cell extract. The quantitation for the decapping efficiency of each protein is presented as the percentage decapping using ImageQuant 5.2 software. The standard m7Gppp and positive control are shown at left. rDcpS are wild type control second from left. 32P-labeled vii methylated cap structure (m7Gpppp) is used as substrate where red colour "p" in m 7 GpppG represented labelled phosphate and m7Gp as product of DcpS catalyzed reaction. 4.18 Western blot analysis showing expression concentration of DcpS in lymphoblast cell lines of generated from patient with homozygous 15 Amino Acid insertion in lane 1 and 4 and heterozygous individuals of Family A in lane 2 and 3. 293T was used for positive control and GAPDH as loading control. 4.19 Pedigree of Family B with autosomal recessive mental retardation where squares represent male and square are used for female. Completely filled squares and circled are for affected whereas unfilled squares and circles shows unaffected individuals. Squares and Circles with dots show carriers. Double lines show consanguineous marriage. Crossed lines show deceased ones. 4.20 Facial images of affected individual (II-4 and III-3) of Family B which did not show any facial dysmorphism. 4.21 Whole Genome Homozygosity image obtained from Homozygosity mapper of Family B showed significant homozygous peaks on chromosome 01, 05, 07, 10, 11, 14 and 15. Homozygus regions are represented in red lines peaks and heterozygous regions are with black peaks. 4.22 (A) The dChip analysed image of SNP marker on viii chromosomes 01, (B) Chromosome 05, (C) chromsome 07, (D) Crhomosome 10, (E) Chromsome 11, (F) chromosome 14 and (G) Chromosome 15. The column represents individual Data (II:4, III:3 and III:4 are affected and III:2 is normal) and SNP data is shown in rows The blue colour depicts homozygous regions and yellow colour shows heterozygous region. 4.23 UCSC genome browser view of the 7p12.1-p11.2 locus 4.24 Whole Exome Sequence data showing the substitution of C with T. 4.25 The sequencing result of PSPH gene of affected (II:4 and III:3 and III-4) and normal individuals (II:1, II:2 and III:2). The diagram A) and B) shows the C>T mutation in two affected (II-4 and III-4) individuals C) whereas one affected (III-3) was heterozygous for this mutation. D) Sequence of normal individual (III-2) was also heterozygous. 4.26 Pedigree of Family C with autosomal recessive mental retardation where squares represent male and square are used for female. Completely filled squares and circled are for affected whereas unfilled squares and circles shows unaffected individuals. Double lines show marriages between cousins and for non cousin marriage single is used. Crossed lines show deceased ones.
American Journal of Medical Genetics Part B: Neuropsychiatric Genetics, 2012
We used whole-genome exon-targeted oligonucleotide array comparative genomic hybridization (array CGH) in a cohort of 256 patients with developmental delay (DD)/ intellectual disability (ID) with or without dysmorphic features, additional neurodevelopmental abnormalities, and/or congenital malformations. In 69 patients, we identified 84 nonpolymorphic copy-number variants, among which 41 are known to be clinically relevant, including two recently described deletions, 4q21.21q21.22 and 17q24.2. Chromosomal microarray analysis revealed also 15 potentially pathogenic changes, including three rare deletions, 5q35.3, 10q21.3, and 13q12.11. Additionally, we found 28 copy-number variants of unknown clinical significance. Our results further support the notion that copy-number variants significantly contribute to the genetic etiology of DD/ID and emphasize the efficacy of the detection of novel candidate genes for neurodevelopmental disorders by whole-genome array CGH.
The genetic landscape of infantile spasms
Infantile spasms (IS) is an early-onset epileptic encephalopathy of unknown etiology in ∼40% of patients. We hypothesized that unexplained IS cases represent a large collection of rare single-gene disorders. We investigated 44 children with unexplained IS using comparative genomic hybridisation arrays (aCGH) (n = 44) followed by targeted sequencing of 35 known epilepsy genes (n = 8) or whole-exome sequencing (WES) of familial trios (n = 18) to search for rare inherited or de novo mutations. aCGH analysis revealed de novo variants in 7% of patients (n = 3/44), including a distal 16p11.2 duplication, a 15q11.1q13.1 tetrasomy and a 2q21.3-q22.2 deletion. Furthermore, it identified a pathogenic maternally inherited Xp11.2 duplication. Targeted sequencing was informative for ARX (n = 1/14) and STXBP1 (n = 1/8). In contrast, sequencing of a panel of 35 known epileptic encephalopathy genes (n = 8) did not identify further mutations. Finally, WES (n = 18) was very informative, with an excess of de novo mutations identified in genes predicted to be involved in neurodevelopmental processes and/or known to be intolerant to functional variations. Several pathogenic mutations were identified, including de novo mutations in STXBP1, CASK and ALG13, as well as recessive mutations in PNPO and ADSL, together explaining 28% of cases (5/18). In addition, WES identified 1-3 de novo variants in 64% of remaining probands, pointing to several interesting candidate genes. Our results indicate that IS are genetically heterogeneous with a major contribution of de novo mutations and that WES is significantly superior to targeted re-sequencing in identifying detrimental genetic variants involved in IS.
Novel European SLC1A4 variant: infantile spasms and population ancestry analysis
Journal of human genetics, 2016
SLC1A4 deficiency is a recently described neurodevelopmental disorder associated with microcephaly, global developmental delay, abnormal myelination, thin corpus callosum and seizures. It has been mainly reported in the Ashkenazi-Jewish population with affected individuals homozygous for the p.Glu256Lys variant. Exome sequencing performed in an Irish proband identified a novel homozygous nonsense SLC1A4 variant [p.Trp453*], confirming a second case of SLC1A4-associated infantile spasms. As this is the first European identified, population ancestry analysis of the Exome Aggregation Consortium database was performed to determine the wider ethnic background of SLC1A4 deficiency carriers. p.Glu256Lys was found in Hispanic and South Asian populations. Other potential disease-causing variants were also identified. Investigation for SLC1A4 deficiency should be performed regardless of ethnicity and extend to include unexplained early-onset epileptic encephalopathy.Journal of Human Genetics ...
Progress in Mapping Human Epilepsy Genes
Epilepsia, 1994
Summary: The chromosomal loci for seven epilepsy genes have been identified in chromosomes lq, 6p, 8q, 16p, 20q, 21q, and 22q. In 1987, the first epilepsy locus was mapped in a common benign idiopathic generalized epilepsy syndrome, juvenile myoclonic epilepsy (JME). Properdin factor or Bf, human leukocyte antigen (HLA), and DNA markers in the HLA-DQ region were genetically linked to JME and the locus, named EJM1, was assigned to the short arm of chromosome 6. Our latest studies, as well as those by White-house et al., show that not all families with JME have their genetic locus in chromosome 6p, and that childhood absence epilepsy does not map to the same EJM1 locus. Recent results, therefore, favor genetic heterogeneity for JME and for the common idiopathic generalized epilepsies. Heterogeneity also exists in benign familial neonatal convulsions, a rare form of idiopathic generalized epilepsy. Two loci are now recognized; one in chromosome 20q (EBN1) and another in chromosome 8q. Heterogeneity also exists for the broad group of debilitating and often fatal progressive myoclonus epilepsies (PME). The gene locus (EPMI) for both the Baltic and Mediterranean types of PME or Unverricht-Lundborg disease is the same and is located in the long arm of chromosome 21. Lafora type of PME does not map to the same EPMI locus in chromosome 21. PME can be caused by the juvenile type of Gaucher's disease, which maps to chromosome lq, by the juvenile type of neuronal ceroid lipofuscinoses (CLN3), which maps to chromosome 16p, and by the “cherry-red-spot-myoclonus” syndrome of Guazzi or sialidosis type I, which has been localized to chromosome 10. A point mutation in the mitochondrial tRNALys coding gene can also cause PME in children and adults (MERFF).
The Genetic Landscape of Epilepsy of Infancy with Migrating Focal Seizures
Annals of Neurology, 2019
Objective: Epilepsy of infancy with migrating focal seizures (EIMFS) is one of the most severe developmental and epileptic encephalopathies. We delineate the genetic causes and genotype-phenotype correlations of a large EIMFS cohort. Methods: Phenotypic and molecular data were analyzed on patients recruited through an international collaborative study. Results: We ascertained 135 patients from 128 unrelated families. 93/135 (69%) had causative variants (42/55 previously reported) across 23 genes, including 9 novel EIMFS genes: de novo dominant GABRA1, GABRB1, ATP1A3; X-linked CDKL5, PIGA; and recessive, ITPA, AIMP1, KARS, WWOX. The most frequently implicated genes were KCNT1 (36/135, 27%) and SCN2A (10/135, 7%). Mosaicism occurred in two probands (SCN2A, GABRB3) and three unaffected mothers (KCNT1). Median age of seizure onset was 4 weeks, with earlier onset in the SCN2A, KCNQ2, and BRAT1 groups. Epileptic spasms occurred in 22% patients. 127 patients had severe to profound developmental impairment. All but 7 patients had ongoing seizures. Additional features included microcephaly, movement disorders, spasticity, and scoliosis. Mortality occurred in 33% at median age 2 years 7 months. Interpretation: We identified a genetic cause in 69% of patients with EIMFS. We highlight the genetic heterogeneity of EIMFS with 9 newly implicated genes, bringing the total number to 33. Mosaicism was observed in probands and parents, carrying critical implications for recurrence risk. EIMFS pathophysiology involves diverse This article is protected by copyright. All rights reserved. molecular processes from gene and protein regulation to ion channel function and solute trafficking.
Genetics in Medicine, 2017
Purpose: Mosaicism probably represents an underreported cause of genetic disorders due to detection challenges during routine molecular diagnostics. The purpose of this study was to evaluate the frequency of mosaicism detected by next-generation sequencing in genes associated with epilepsy-related neurodevelopmental disorders. Methods: We conducted a retrospective analysis of 893 probands with epilepsy who had a multigene epilepsy panel or whole-exome sequencing performed in a clinical diagnostic laboratory and were positive for a pathogenic or likely pathogenic variant in one of nine genes (CDKL5, GABRA1, GABRG2, GRIN2B, KCNQ2, MECP2, PCDH19, SCN1A, or SCN2A). Parental results were available for 395 of these probands. Results: Mosaicism was most common in the CDKL5, PCDH19, SCN2A, and SCN1A genes. Mosaicism was observed in GABRA1, GABRG2, and GRIN2B, which previously have not been reported to have mosaicism, and also in KCNQ2 and MECP2. Parental mosaicism was observed for pathogenic variants in multiple genes including KCNQ2, MECP2, SCN1A, and SCN2A. Conclusion: Mosaic pathogenic variants were identified frequently in nine genes associated with various neurological conditions. Given the potential clinical ramifications, our findings suggest that next-generation sequencing diagnostic methods may be utilized when testing these genes in a diagnostic laboratory.
Human Mutation, 2014
Spinal muscular atrophy (SMA) is a neuromuscular autosomal recessive disease characterized by progressive muscle weakness and atrophy combined with motor neuron degeneration caused by mutations in the SMN 1 gene locus (5q11.2-13.2). Rett syndrome (RS) is an X-linked dominant neurodevelopmental disorder caused by mutations in MECP2 (Xq28) and characterized by normal development until 6-12 months of age, followed by regression with loss of acquired skills, gradual onset of microcephaly, stereotypic hand movements and psychomotor delay. We report a 6-year-old girl who, at 2 years of age, presented with hypotonia, psychomotor delay, amyotrophy and areflexia of the lower extremities. Molecular DNA analysis (PCR-RFLP's) for SMA type II revealed that both exons 7 and 8 of SMN 1 gene were deleted. Over the past 4 years, onset of stereotypic hand-washing movements, epileptic seizures, microcephaly, hyperventilation/breath-holding attacks and severe psychomotor delay raised the suspicion of the coexistence of RS. DNA analysis (DGGE and sequencing) identified the hotspot missense mutation R306C (c.916C4T) in exon 4 of the MECP2 gene. The coinheritance of SMA and RS, two rare monogenic syndromes in the same patient, has not been previously reported. Thorough clinical evaluation in combination with DNA analysis, allowed accurate diagnosis, providing valuable information for the genetic counseling of the family.