Physical map and haplotype analysis of 16q-linked autosomal dominant cerebellar ataxia (ADCA) type III in Japan

 Autosomal dominant cerebellar ataxia (ADCA) is a group of heterogeneous neurodegenerative disorders. We previously mapped a gene locus for ADCA with pure cerebellar syndrome (ADCA type III) to a 3-cM region in chromosome 16q, and found a common haplotype among affected individuals. This region was exactly within the locus for another ADCA, spinocerebellar ataxia type 4 (SCA4). To identify the gene causing 16q-linked ADCA type III, we constructed a contig with 38 bacterial artificial chromosome clones between D16S3043 and D16S3095. The size of this contig was estimated to be 4.8 Mb. We found more than 500 nucleotide tandem repeats, including 9 CAG/CTG repeats in this candidate region, although none of the 94 tandem repeats analyzed were expanded in affected individuals. However, we found 11 new polymorphic markers, giving 22 markers spanning the candidate region. By typing these markers on eight Japanese families with ADCA type III, including two new families, we found that a common “founder” haplotype is seen in a more restricted 3.8-Mb region, spanning markers GGAA05 and D16S3095. We present here a newly refined critical interval of 16q-ADCA type III/SCA4. Data of 11 new DNA markers on 16q22.1 would also be useful for other research of genes mapped to this region. Received: June 25, 2002 / Accepted: November 22, 2002 Correspondence to:H. Mizusawa     

A −16C>T substitution in the 5′ UTR of the puratrophin-1 gene is prevalent in autosomal dominant cerebellar ataxia in Nagano

The molecular bases of autosomal dominant cerebellar ataxia (ADCA) have been increasingly elucidated, but 17–50% of ADCA families still remain genetically undefined in Japan. In this study we investigated 67 genetically undefined ADCA families from the Nagano prefecture, and found that 63 patients from 51 families possessed the –16C>T change in the puratrophin-1 gene, which was recently found to be pathogenic for 16q22-linked ADCA. Most patients shared a common haplotype around the puratrophin-1 gene. All patients with the –16C>T change had pure cerebellar ataxia with middle-aged or later onset. Only one patient in a large, –16C>T positive family did not have this change, but still shared a narrowed haplotype with, and was clinically indistinguishable from, the other affected family members. In Nagano, 16q22-linked ADCA appears to be much more prevalent than either SCA6 or dentatorubral-pallidoluysian atrophy (DRPLA), and may explain the high frequency of spinocerebellar ataxia.Takako Ohata and Kunihiro Yoshida have equally contributed to this work     

Association and synergistic interaction between promoter variants of the DRD4 gene in Japanese schizophrenics

Recent association studies suggest that polymorphisms in the promoter and exon 1 upstream region of the dopamine D4 receptor (DRD4) gene play a functional role in the development of common psychiatric illnesses, although there are also conflicting results. In this study, we re-sequenced this region to identify all genomic variants, and tested them for association with schizophrenia. A total of 570 Japanese schizophrenic cases with matched controls were studied by genotyping all identified/validated common polymorphisms (−1106T>C, −906T>C, −809G>A, −616G>C, −521T>C, −376C>T, −291C>T and 12-bp repeat) and a known microsatellite (120-bp tandem duplication) in the upstream region. A single nucleotide polymorphism (SNP) −809G>A in the promoter region was found to be significantly associated with disease (P=0.018 and 0.032 for allelic and genotypic comparisons, respectively), although not surviving after Bonferroni correction. Logistic regression analysis showed that a combination of the four polymorphisms, −809G>A, −616G>C, −291C>T and the 12-bp repeat, conferred a susceptibility to schizophrenia. These results suggest that the upstream variants have a primary functional effect in the etiology of schizophrenia in the Japanese population. The nucleotide polymorphism data reported is available in the DDBJ/EMBL/GenBank databases under the accession number ss61570833.     

Identification of polymorphisms in the human SHP1 gene

 Because mutations in human SHP1 underlie obesity and diabetes, SHP1 is a candidate gene for human lipodystrophy syndromes. To identify possible disease mutations and/or common single-nucleotide polymorphisms (SNPs), we developed primer pairs to amplify the promoter and coding region of SHP1. We used these pairs to sequence SHP1 in lipodystrophy patients who had no mutations in known lipodystrophy genes, and also in normal control subjects. We found no rare SHP1 coding sequence variants that were exclusive to patients with lipodystrophy. However, we found four polymorphisms, namely, an SNP [−394]C>T in the promoter, a micro-deletion polymorphism [−195]delCTGA in the promoter, a missense SNP 541G>C in exon 1 (which changed the amino acid sequence G171A), and an SNP 903C>T in exon 2. The findings suggest that SHP1 mutations are not commonly seen in patients with lipodystrophy who had no mutations in known disease genes. However, the identification of amplification primers and polymorphisms provides tools to further investigate SHP1 for association with other phenotypes. Received: April 1, 2002 / Accepted: April 22, 2002     

Association analysis of polymorphisms in the upstream region of the human dopamine D4 receptor gene (DRD4) with schizophrenia and personality traits

The human dopamine D4 receptor (DRD4) is of major interest in molecular studies of schizophrenia and personality traits. We examined the association of schizophrenia and polymorphisms in the upstream region of the DRD4 gene (−768G>A in the negative modulator region; −521C>T, −376C>T, and −291C>T in the cell type-specific promoter region; and −616C>G between the two regions) in 208 schizophrenic patients and 210 normal controls. No significant difference in genotype and allele frequencies was observed between the two groups, indicating that these polymorphisms do not make a major contribution to the pathogenesis of schizophrenia. We also studied the association of polymorphisms in the upstream region and a 48-bp repeat polymorphism in exon III of the DRD4 gene with personality traits in 173 Japanese individuals who completed the temperament and character inventory (TCI). The −768G>A polymorphism was significantly associated with reward dependence (P = 0.044), while no significant association was observed between novelty seeking and polymorphisms in the upstream region or the exon III repeat polymorphism of the DRD4 gene. Received: August 28, 2000 / Accepted: October 25, 2000     

Spectrum and prevalence of autosomal dominant spinocerebellar ataxia in Hokkaido,the northern island of Japan: a study of 113 Japanese families

Autosomal dominant cerebellar ataxia (ADCA) is a genetically heterogeneous group of neurodegenerative disorders. To shed further light on the clinical and genetic spectrum of ADCA in Japan, we conducted a study to determine the frequency of a new variety of different subtypes of SCAs among ADCA patients. This current study was carried out from April 1999 to December 2006 on the basis of patients with symptoms and signs of ADCA disorders. PCR and/or direct sequencing were evaluated in a total of 113 families. Among them, 35 families were found to have the mutation associated with SCA6, 30 with SCA3, 11 with SCA1, five with SCA2, five with DRPLA, and one with SCA14. We also detected the heterozygous −16C → T single nucleotide substitution within the puratrophin-1 gene responsible for 16q22.1-linked ADCA in ten families. In this study, unusual varieties of SCA, including 27, 13, 5, 7, 8, 12, 17, and 16 were not found. Of the 113 patients, 14% had as yet unidentified ADCA mutations. The present study validates the prevalence of genetically distinct ADCA subtypes based on ethnic origin and geographical variation, and shows that 16q-linked ADCA has strong hereditary effects in patients with ADCAs in Japan. Rehana Basri, Ichiro Yabe, and Hiroyuki Soma contributed equally to this work.     

A linkage disequilibrium at the candidate gene locus for 16q-linked autosomal dominant cerebellar ataxia type III in Japan

We previously mapped the gene responsible for autosomal dominant cerebellar ataxia (ADCA) type III to a 10.9-cM interval between D16S3089 and D16S515 on chromosome 16q. This region, however, was identical to the candidate locus of spinocerebellar ataxia type 4 (SCA4). In this study, we extended our research to refine the gene locus of the disease by applying linkage disequilibrium with 20 microsatellite DNA markers. With 9 markers flanked by D16S3031 and D16S3107, we found that the affected individuals in six families had a common haplotype on their disease chromosomes. Furthermore, linkage disequilibrium was demonstrated with 5 informative markers: D16S3019 (P = 0.013), D16S3067 (P = 0.008), D16S3141 (P = 0.011), D16S496 (P = 0.032), and D16S3107 (P = 0.000). These results indicate that the disease could have originated from a common ancestor harboring a mutation within a less than 3-cM region between D16S3043 and D16S3095. The founder alleles were also observed in other patients with ADCA type III unrelated to the six families. Received: October 25, 2000 / Accepted: January 5, 2001     

Missense mutations in the AFG3L2 proteolytic domain account for ∼1.5% of European autosomal dominant cerebellar ataxias

Spinocerebellar ataxia type 28 is an autosomal dominant form of cerebellar ataxia (ADCA) caused by mutations in AFG3L2, a gene that encodes a subunit of the mitochondrial m‐AAA protease. We screened 366 primarily Caucasian ADCA families, negative for the most common triplet expansions, for point mutations in AFG3L2 using DHPLC. Whole‐gene deletions were excluded in 300 of the patients, and duplications were excluded in 129 patients. We found six missense mutations in nine unrelated index cases (9/366, 2.6%): c.1961C>T (p.Thr654Ile) in exon 15, c.1996A>G (p.Met666Val), c.1997T>G (p.Met666Arg), c.1997T>C (p.Met666Thr), c.2011G>A (p.Gly671Arg), and c.2012G>A (p.Gly671Glu) in exon 16. All mutated amino acids were located in the C‐terminal proteolytic domain. In available cases, we demonstrated the mutations segregated with the disease. Mutated amino acids are highly conserved, and bioinformatic analysis indicates the substitutions are likely deleterious. This investigation demonstrates that SCA28 accounts for ～3% of ADCA Caucasian cases negative for triplet expansions and, in extenso, to ～1.5% of all ADCA. We further confirm both the involvement of AFG3L2 gene in SCA28 and the presence of a mutational hotspot in exons 15–16. Screening for SCA28, is warranted in patients who test negative for more common SCAs and present with a slowly progressive cerebellar ataxia accompanied by oculomotor signs. Hum Mutat 31:1–8, 2010. © 2010 Wiley‐Liss, Inc.     

A Japanese case of SCA14 with the Gly128Asp mutation

Spinocerebellar ataxia type 14 (SCA14) is a rare form of autosomal dominant cerebellar ataxias caused by mutations in the protein kinase Cγ gene (PRKCG). We have identified a Japanese patient with SCA14 who carried the Gly128Asp mutation in PRKCG. She first noticed gait unsteadiness at around age 42, and then her gait ataxia worsened very slowly for more than 20 years. At age 62, she was still ambulatory, although cerebellar ataxia was clinically evident. She is the second patient identified with the G128D mutation. Both patients with this mutation showed pure cerebellar ataxia. With only two families with SCA14 found in Japan prior to this study, the clinical features and disease-causing mutations in PRKCG are heterogeneous in the same ethnic background.     

Mutation analysis of the ALD gene in seven Japanese families with X-linked adrenoleukodystrophy

 The childhood cerebral form of X-linked adrenoleukodystrophy (X-ALD) is a severe congenital metabolic disease without a definite effective therapy except for hematopoietic stem cell transplantation in the appropriate disease stage. Seven Japanese families with X-ALD were analyzed for mutations in the ALD gene (ALD). Of the seven families, three were referred to us for prenatal diagnosis, four for carrier detection, and three for confirmation diagnosis of patients. By nucleotide sequencing and/or restriction analysis, all the subjects to be examined were successfully diagnosed. Six different missense mutations in ALD were identified. There was a G→A substitution (G512S) in two unrelated families, and a G→A (R617H), a C→T (R660W), a G→C (R163P), a C→T (S606L), or a G→A (G116E) substitution in each of the other five families. Among the six substitutions, five were those reported previously and the other was a novel mutation. In three families, prenatal diagnosis was carried out after genetic counseling. Received: September 9, 2002 / Accepted: November 26, 2002 Correspondence to:T. Matsumoto     

Two novel mutations and coexistence of the 991C.T and the 1339C.T mutation on a single allele in the coproporphyrinogen oxidase gene in Swedish patients with hereditary coproporphyria

 Hereditary coproporphyria (HCP) is an autosomal dominant disorder, resulting from a partial deficiency of the enzyme coproporphyrinogen oxidase (CPO). This enzyme catalyzes the sixth step of the heme biosynthetic pathway, and mutations in the CPO gene have been coupled to HCP. The present study was undertaken to identify disease-producing mutations in the CPO gene in nine Swedish families with HCP. Exon 1 of the CPO gene of the nine probands was analyzed directly by sequencing, and exons 2–7 were screened by denaturating gradient gel electrophoresis, followed by sequencing of exons showing abnormal band pattern. Mutations were detected in five of the nine families. In two of these families, the novel mutations 623C>T (S208F, exon 2) and 982C>T (R328C, exon 5) were identified, respectively. In the affected members of the other three families, the previously reported mutations 991C>T (R331W, exon 5) and 1339C>T (R447C, exon 7) were shown to coexist on one allele. The present study contributes 2 novel mutations to the 34 that have been previously reported to cause HCP. In addition, this is the first report on patients carrying two HCP-coupled mutations on one allele. Received: March 8, 2002 / Accepted: April 24, 2002     

Identification of single-nucleotide polymorphisms in the human LPIN1 gene

 Because mutations in the murine analog of human LPIN1 cause lipodystrophy in mice, LPIN1 is a candidate gene for human lipodystrophy syndromes. To identify possible disease mutations and/or common single-nucleotide polymorphisms (SNPs), we developed primer pairs to amplify the 21 exons of LPIN1. We used these primer pairs to sequence LPIN1 in lipodystrophy patients who had no mutations in known lipodystrophy genes, and also in normal control subjects. We found no rare LPIN1 coding sequence variants that were exclusive to patients with lipodystrophy. However, we found four silent SNPs, namely, +17C>T in exon 3, 935C>T in exon 5, and 1040G>A and 1079G>C in exon 6, and one nonsynonymous SNP, namely, 2211C>T (P616S) in exon 15. The findings suggest that LPIN1 mutations are not commonly seen in patients with lipodystrophy who had no mutations in known disease genes. However, the identification of amplification primers and SNPs provides tools to further investigate LPIN1 for association with other phenotypes. Received: January 10, 2002 / Accepted: March 15, 2002     

Mutations of the puratrophin-1 (PLEKHG4) gene on chromosome 16q22.1 are not a common genetic cause of cerebellar ataxia in a European population

Autosomal dominant cerebellar ataxia (ADCA) is a genetically heterogeneous group of neurodegenerative disorders with overlapping clinical presentation. Recently, a single nucleotide substitution in the 5-untranslated region (UTR) of the puratrophin-1 (PLEKHG4) gene on chromosome 16q22.1 has been shown to be associated with ADCA in 52 unrelated Japanese families. As this mutation has so far not been investigated in other populations, we have screened 537 European patients with a clinical diagnosis of cerebellar ataxia for this specific nucleotide substitution. The mutation was not identified in our cohort. In addition, we screened the complete 5-UTR as well as the entire coding region of this gene in 120 patients for variations that might account for their clinical symptoms. Several new rare variations were found. For none of the variations could an obvious pathogenetic relevance be postulated at this point, albeit some findings should be followed up in additional populations and by functional assays. We conclude that mutations of the puratrophin-1 gene are not a common cause of hereditary ataxia in our Caucasian population.     

Congenital dyserythropoietic anemia type II (CDAII) is caused by mutations in the SEC23B gene

Congenital dyserythropoietic anemia type II (CDAII) is an autosomal recessive disease characterized by ineffective erythropoiesis, hemolysis, erythroblast morphological abnormalities, and hypoglycosylation of some red blood cell (RBC) membrane proteins. Recent studies indicated that CDAII is caused by a defect disturbing Golgi processing in erythroblasts. A linkage analysis located a candidate region on chromosome 20, termed the CDAN2 locus, in the majority of CDAII patients but the aberrant gene has not so far been elucidated. We used a proteomic‐genomic approach to identify SEC23B as the candidate gene for CDAII by matching the recently published data on the cytoplasmic proteome of human RBCs with the chromosomic localization of CDAN2 locus. Sequencing analysis of SEC23B gene in 13 CDAII patients from 10 families revealed 12 different mutations: six missense (c.40C>T, c.325G>A, c.1043A>C, c.1489C>T, c.1808C>T, and c.2101C>T), two frameshift (c.428_428delAinsCG and c.1821delT), one splicing (c.689+1G>A), and three nonsense (c.568C>T, c.649C>T, and c.1660C>T). Mutations c.40C>T and c.325G>A were detected in unrelated patients. SEC23B is a member of the Sec23/Sec24 family, a component of the COPII coat protein complex involved in protein transport through membrane vesicles. Abnormalities in this gene are likely to disturb endoplasmic reticulum (ER)‐to‐Golgi trafficking, affecting different glycosylation pathways and ultimately accounting for the cellular phenotype observed in CDAII. Hum Mutat 30:1–7, 2009. © 2009 Wiley‐Liss, Inc.     

The association of RAR‐related orphan receptor A (RORA) gene polymorphisms with the risk of asthma

Asthma is a common, heterogeneous chronic respiratory disease characterized by chronic inflammation of the airway, airway hyperreactivity, and airway remodeling. The RAR‐related orphan receptor A (RORA) gene has been identified for the pathogenesis of asthma. The purpose of this research was to investigate the relationship between RORA gene polymorphisms and asthma susceptibility in the Chinese Zhuang population. This was a case–control study including 231 children with asthma and 343 healthy controls. The RORA gene polymorphisms were measured by the polymerase chain reaction–ligase detection reaction genotyping assays and confirmed by sequencing. The distribution of the genotype frequencies of the RORA rs11071559 C>T was significantly different in the group of cases and the healthy children (P < 0.05). By haplotype analyses, the haplotype TT (rs7164773/rs11071559) was statistically significant between asthmatics and nonasthmatics, but the association was not significant after correction for multiple comparisons. Our results provided evidence that the RORA rs11071559C>T polymorphism was associated with an elevated susceptibility to pediatric asthma in the Chinese Zhuang population.     

A missense founder mutation in VLDLR is associated with Dysequilibrium Syndrome without quadrupedal locomotion

ABSTRACT: BACKGROUND: Dysequilibrium syndrome is a genetically heterogeneous condition that combines autosomal recessive, nonprogressive cerebellar ataxia with mental retardation. The condition has been classified into cerebellar ataxia, mental retardation and disequilibrium syndrome types 1 (CAMRQ1), 2 (CAMRQ2) and 3 (CAMRQ3) and attributed to mutations in VLDLR, CA8 and WDR81 genes, respectively. Quadrupedal locomotion in this syndrome has been reported in association with mutations in all three genes. METHODS: SNP mapping and candidate gene sequencing in one consanguineous Omani family from the United Arab Emirates with cerebellar hypoplasia, moderate mental retardation, delayed ambulation and truncal ataxia was used to identify the mutation. In a second unrelated consanguineous Omani family, massively parallel exonic sequencing was used. RESULTS: We identified a homozygous missense mutation (c.2117 G > T, p.C706F) in the VLDLR gene in both families on a shared affected haplotype block.This is the first reported homozygous missense mutation in VLDLR and it occurs in a highly conserved residue and predicted to be damaging to protein function. CONCLUSIONS: We have delineated the phenotype associated with dysequilibrium syndrome in two Omani families and identified the first homozygous missense pathogenic mutation in VLDLR gene with likely founder effect in the southwestern part of the Arabian Peninsula.     

Polymorphism of extracellular superoxide dismutase (EC-SOD) gene: relation to the mutation responsible for high EC-SOD level in serum

Summary Extracellular superoxide dismutase (EC-SOD) with amino acid substitution R213G generated by the nucleotide substitution 760C→G in the heparin binding domain is responsible for the high EC-SOD level in serum. We identified the two DNA polymorphic sites in the coding region of EC-SOD gene related to the 760C→G and determined the allele frequencies. The polymorphisms were A and G at nucleotide position (nt.) 241 and C and T at nt. 280 near the N-terminal. The haplotype frequencies in Japanese were 241A280C: 0.45, 241G280T: 0.37, and 241G280C: 0.18. The haplotype of 241A280T did not exist. The mutation 760C→G must occur on the allele having the haplotype of 241G280T.     

Functional promoter polymorphism in SREBP cleavage-activating protein (SCAP)

 We report the identification of a loss-of-function −11C>T promoter mutation in the gene encoding the sterol regulatory element binding protein cleavage-activating protein (SCAP). The −11T allele was associated with a marked reduction in promoter activity in a luciferase-based expression system. We also report additional common single-nucleotide polymorphisms in the SCAP promoter and coding sequence that were identified by using direct sequencing to screen the genomic DNA of subjects with combined hyperlipidemia. These markers might be useful for studies of association with metabolic phenotypes. Received: May 3, 2002 / Accepted: June 11, 2002     

Missense variants in the X‐linked gene PRPS1 cause retinal degeneration in females

Retinal dystrophies are a heterogeneous group of disorders of visual function leading to partial or complete blindness. We report the genetic basis of an unusual retinal dystrophy in five families with affected females and no affected males. Heterozygous missense variants were identified in the X‐linked phosphoribosyl pyrophosphate synthetase 1 (PRPS1) gene: c.47C > T, p.(Ser16Phe); c.586C > T, p.(Arg196Trp); c.641G > C, p.(Arg214Pro); and c.640C > T, p.(Arg214Trp). Missense variants in PRPS1 are usually associated with disease in male patients, including Arts syndrome, Charcot–Marie–Tooth, and nonsyndromic sensorineural deafness. In our study families, affected females manifested a retinal dystrophy with interocular asymmetry. Three unrelated females from these families had hearing loss leading to a diagnosis of Usher syndrome. Other neurological manifestations were also observed in three individuals. Our data highlight the unexpected X‐linked inheritance of retinal degeneration in females caused by variants in PRPS1 and suggest that tissue‐specific skewed X‐inactivation or variable levels of pyrophosphate synthetase‐1 deficiency are the underlying mechanism(s). We speculate that the absence of affected males in the study families suggests that some variants may be male embryonic lethal when inherited in the hemizygous state. The unbiased nature of next‐generation sequencing enables all possible modes of inheritance to be considered for association of gene variants with novel phenotypic presentation.     

Novel polymorphisms in the upstream region of the human dopamine D4 receptor (DRD4) gene

We found nine novel polymorphisms in the upstream region of the human dopamine D4 receptor (DRD4) gene of Japanese by direct sequencing. These polymorphisms are −809G > A, −768G > A, −616C > G, −603T > del, −602G > del, −600G > C, −376C > T, −291C > T, and −128G > T. One known polymorphism, −521C > T, was also recognized. Six of these sites were identified as restriction fragment length polymorphisms (RFLPs). Received: June 11, 1999 / Accepted: June 23, 1999