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PubMed1985

Molecular consequences of specific intron mutations on yeast mRNA splicing in vivo and in vitro.

We have altered the TACTAAC sequence in the yeast CYH2m gene intron to TACTACC. This mutation changes the nucleotide at the normal position of the branch in intron RNA lariats produced during pre-mRNA splicing, and it prevents splicing in vivo. In a yeast pre-mRNA splicing system, CYH2m pre-mRNA carrying the TACTACC mutation is not specifically cut or rearranged in any way. Substitution of an A for the first G of the CYH2m intron, converting the highly conserved GTATGT 5' splice site sequence to ATATGT, also blocks intron excision in vivo and in vitro: pre-mRNA carrying this mutation was still cut normally at the mutant 5' splice site in vitro, to give authentic exon 1 and an intron-exon 2 lariat RNA with an A-A 2'-5' phosphodiester linkage at the branch point. This lariat RNA is a dead-end product. The subsequent cleavage at the 3' splice site is therefore sensitive to the sequence of the 5' end of the intron attached at the branch point.

Base Sequence↗

PubMed1993

Comparison of enzyme and DNA analysis in a Tay-Sachs disease carrier screening program.

Tay-Sachs disease (GM2 gangliosidosis, type 1; TSD) is an autosomal recessive GM2 gangliosidosis resulting from the deficient activity of the lysosomal hydrolase beta-hexosaminidase A (Hex A). With a carrier frequency estimated at 1 in 25, it is a common lysosomal disorder in the Ashkenazi Jewish population. Tay-Sachs disease has provided the prototype for the prevention of severe recessive genetic diseases. Molecular analysis of the Hex A gene (HEXA) of Ashkenazi Jewish individuals affected with Tay-Sachs disease revealed that three common mutations cause the infantile and adult onset forms of the disease; a four base insertion in exon 11, a splice junction mutation in intron 12 and a point mutation in exon 7 (G269S). A study was undertaken to determine whether mutation analysis would be useful in TSD screening programs in identifying carriers and clarifying the status of individuals whose enzyme assays are inconclusive. Ashkenazi Jewish individuals who had been diagnosed as carriers, inconclusives by enzyme assay and non-carriers with low normal enzyme levels in the Mount Sinai Tay-Sachs Disease Prevention Program were examined for the presence of the three mutations using polymerase chain reaction (PCR) and allele specific oligonucleotide (ASO) hybridization. The insertion mutation was present in 29 of 34 carriers and 2 of 36 inconclusive individuals, the splice junction mutation was found in 4 of 34 carriers and the G269S mutation was found in 1 of 34 carriers. Of the 313 non-carrier individuals with normal enzyme activity in the lower normal range, one was positive for the splice junction mutation.(ABSTRACT TRUNCATED AT 250 WORDS)

Base Sequence↗

PubMed1998

Repeat-induced point mutations in Pad-1, a putative RNA splicing factor from Neurospora crassa, confer dominant lethal effects on ascus development.

We describe the characterization of a gene, Pad-1, from Neurospora crassa which displays sequence characteristics of the RS class of hnRNA-binding proteins (hnRNP) and mRNA splicing factors. This is the first report of the isolation of a putative hnRNP gene from N. crassa. PAD-1 showed 30% identity and 57% similarity to a protein, HCC1, which was isolated using autoantibodies from patients suffering from hepatocellular carcinoma. Both HCC1 and PAD-1 show amino acid sequence similarities to the human splicing factor, U2AF65. Mutations induced in Pad-1 by repeat-induced point (RIP) mutation show dominant effects on ascus and ascospore formation, a novel phenotypic class of RIP mutants. A mutant isolated from the Pad-1 RIP cross displayed a severe vegetative growth defect and dominant effects on ascus development, indicating that Pad-1 is essential for both asexual and sexual development.

Amino Acid Sequence↗

PubMed2003

A recessive mutant of Drosophila Clock reveals a role in circadian rhythm amplitude.

The transcription factor Clock (Clk) plays a critical role in animal circadian rhythms. Genetic studies defining its function have relied on two dominant negative alleles, one in Drosophila and one in mice. Here we describe a novel recessive allele of Drosophila Clock, Clk(ar). Homozygous Clk(ar) flies are viable and behaviorally arrhythmic. The Clk(ar) phenotype is caused by a splice site mutation that severely disrupts splicing and reduces Clk activity. Despite the behavioral arrhythmicity, molecular oscillations are still detectable in Clk(ar) flies. Transcription analysis indicates potent effects of Clk(ar) on levels and amplitude of transcriptional oscillations. Taken together with other data, we propose that Clk makes a major contribution to the strength and amplitude of circadian rhythms.

Alleles↗

PubMed2001

Thirty-three novel COL1A1 and COL1A2 mutations in patients with osteogenesis imperfecta types I-IV.

Osteogenesis imperfecta (OI) is a heritable disease of bone characterized by low bone mass and bone fragility. Six different types of OI have been described to date, based on clinical phenotype and histological findings. The genetic defect in many patients with OI types I-IV is due to mutations in the genes encoding type I collagen, while patients with OI types V and VI show no evidence of mutations in the COL1A1/COL1A2 genes. Here we report thirty-three novel mutations in patients with types I-IV OI. Sixteen mutations were in COL1A1 and seventeen were in COL1A2. Most mutations resulted in substitutions for glycine: one of these, a doublet GG>CC transversion, created a unique Gly-->Pro missense mutation in the triple helical domain of COL1A2. Two rare triple helical Gly-->Glu substitutions in COL1A2 are also described. In addition, there were six single-base deletion mutations resulting in frameshifts, seven splice junction mutations, and a 9-bp triple helix insertion associated with a severe (OI II) phenotype. The variety of mutations described in the COL1A1/COL1A2 genes giving rise to an OI phenotype is in accordance with the clinical heterogeneity of the disease. Hum Mutat 17:434, 2001.

Alternative Splicing↗

PubMed2005

New calcium channel mutations predict aberrant RNA splicing in episodic ataxia.

Episodic ataxia type 2 (EA2) is an autosomal dominant channelopathy characterized by paroxysmal cerebellar ataxia. Previous studies suggest that most EA2 cases are associated with mutations in the alpha1A subunit of the P/Q-type voltage-gated calcium channel gene CACNA1A. In a UK national study, the authors analyzed 15 index cases with typical EA2 and identified two unreported intronic mutations that predict aberrant splicing.

Adolescent↗

PubMed2005

Genetic studies of 20 Japanese families of dystrophic epidermolysis bullosa.

Dystrophic EB (DEB) is clinically characterized by mucocutaneous blistering in response to minor trauma, followed by scarring and nail dystrophy, and is caused by mutations in the COL7A1 gene encoding type VII collagen. DEB is inherited in either an autosomal dominant (DDEB) or recessive (RDEB) fashion. DDEB basically results from a glycine substitution mutation within the collagenous domain on one COL7A1 allele, while a combination of mutations such as premature stop codon, missense, and splice-site mutations on both alleles causes RDEB. In this study, mutation analysis was performed in 20 distinct Japanese DEB families (16 RDEB and four DDEB). The result demonstrated 30 pathogenic COL7A1 mutations with 16 novel mutations, which included four missense, five nonsense, one deletion, two insertion, one indel, and three splice-site mutations. We confirmed that Japanese COL7A1 mutations were basically family specific, although three mutations, 5818delC, 6573 + 1G > C, and E2857X, were recurrent based on previous reports. Furthermore, the Q2827X mutation found in two unrelated families would be regarded as a candidate recurrent Japanese COL7A1 mutation. The study furthers our understanding of both the clinical and allelic heterogeneity displayed in Japanese DEB patients.

Adult↗

PubMed1996

Molecular analysis of the presenilin 1 (S182) gene in "sporadic" cases of Alzheimer's disease: identification and characterisation of unusual splice variants.

Mutations of the presenilin 1 (PS-1) gene at the Alzheimer's disease (AD) FAD3 locus on chromosome 14q24.3 are responsible for the majority of familial early-onset AD. As genes responsible for familial forms of AD are obvious candidates for further investigation in "sporadic" disease, we performed a molecular analysis of PS-1 transcripts extracted from brain tissues of a series of histologically confirmed cases of "sporadic" AD (n=10) and also from histologically "normal" (non-Alzheimer) age-matched brain controls (n=5). No sequence changes in the PS-1 coding sequence were detected after analysis by reverse transcription-PCR. This suggests that the frequency of mutations in the PS-1 (S182) coding region in "sporadic" Alzheimer's disease in very low. However, we demonstrated that the PS-1 gene is highly variably spliced. One splice variant involves the 5' untranslated region of the PS-1 gene only and hence encodes for normal PS-1. Six further splice variants involve coding regions of the PS-1 gene and result in truncated proteins lacking specific transmembrane domains. Most of these variants do not coincide with recognized sites of introns in the PS-1 gene. One of these variants, resulting in the loss of transmembrane domain TM-VII, was found only in an AD patient.

Alternative Splicing↗

PubMed2005

Limb girdle muscular dystrophy in a sibling pair with a homozygous Ser606Leu mutation in the alternatively spliced IS2 region of calpain 3.

Previous family studies revealed a large number of calpain 3 ( CAPN3 ) mutations that cause recessive forms of limb girdle muscular dystrophy (LGMD2A) with selective atrophy of the proximal limb muscles. Correlations between the nature and site of a particular mutation and its corresponding phenotype, however, can only be established from homozygous mutations, which are particularly rare in the alternatively spliced NS, IS1 and IS2 regions of CAPN3. Here we identified a sibling pair with LGMD2A-type muscular dystrophy caused by a homozygous Ser606Leu (S606L) substitution in the IS2 linker domain. Normal protein levels, unaltered myofibrillar targeting and conserved calcium-induced autocatalytic activity of the mutated protein could be demonstrated in muscle biopsies from one patient. Despite this inconspicuous modification of the IS2 linker between domains III and IV, both patients developed signs and symptoms of the disease within their second decade of life. The unexpected severity of the clinical manifestation points to the high relevance of the calpain 3-specific IS2 segment between domains III and IV. We conclude that the structural motif around the Ser606 residue represents an important functional site that may regulate the transient activation and limited proteolysis of calpain 3.

Age of Onset↗

PubMed2005

Mutation analysis of SPG4 and SPG3A genes and its implication in molecular diagnosis of Korean patients with hereditary spastic paraplegia.

BACKGROUND: Hereditary spastic paraplegia (HSP), a genetically and clinically heterogeneous group of neurodegenerative disorders, is characterized by progressive lower limb weakness and spasticity. Among the 8 loci associated with the autosomal dominant uncomplicated HSP (AD-HSP), the spastin (SPG4) and atlastin (SPG3A) genes have been known to account for approximately 40% and 10% of all cases, respectively. OBJECTIVE: To investigate the contribution of these 2 genes in the occurrence of HSP in Korean patients. DESIGN: Clinical and genetic study. SETTING: Tertiary care center. PATIENTS: Eighteen patients with uncomplicated HSP (11 AD and 7 sporadic) underwent screening for gene mutation. MAIN OUTCOME MEASURES: Mutations in the SPG4 and SPG3A genes as detected by direct sequencing of all coding exons and flanking intronic sequences. RESULTS: We identified 8 different SPG4 mutations, 7 of which have not been reported elsewhere. Among the detected mutations were 3 missense mutations, 2 in-frame deletions, 2 frameshift mutations, and 1 splice-site mutation. No mutation was found in the SPG3A gene. CONCLUSION: Compared with previous studies, a higher frequency of SPG4 gene mutations in AD-HSP (7/11; 64%) was observed, suggesting that a mutation analysis for the SPG4 gene might be helpful for molecular diagnosis of AD-HSP in Korean patients.

Adenosine Triphosphatases↗

PubMed2000

Identification of 5 novel mutations in the AGXT gene.

In order to identify additional genotypes in primary hyperoxaluria type 1, we sequenced the AGXT genes of 9 patients. We report 5 new mutations. Three are splice-site mutations situated at the end of intron 4 and 8 (647-1G>A, 969-1G>C, 969-3C>G), one is a missense mutation in exon 5 (D183N), and one is a short duplication in exon 2 (349ins7). Their consequence is always a lack of enzymatic activity of the Alanine-Glyoxylate Aminotransferase (AGT); for 4 of them, we were able to deduce that they were associated to the absence of AGT protein. These mutations are rare, as they have been found on one allele in our study (except 969-3C>G present in 2 unrelated families), and have not been previously reported.

Adult↗

PubMed2000

Genetic variation in ICF syndrome: evidence for genetic heterogeneity.

ICF syndrome is a rare autosomal recessive immunoglobulin deficiency, sometimes combined with defective cellular immunity. Other features that are frequently observed in ICF syndrome patients include facial dysmorphism, developmental delay, and recurrent infections. The most diagnostic feature of ICF syndrome is the branching of chromosomes 1, 9, and 16 due to pericentromeric instability. Positional candidate cloning recently discovered the de novo DNA methyltransferase 3B (DNMT3B) as the responsible gene by identifying seven different mutations in nine ICF patients. DNMT3B specifically methylates repeat sequences adjacent to the centromeres of chromosome 1, 9, and 16. Our panel of 14 ICF patients was subjected to mutation analysis in the DNMT3B gene. Mutations in DNMT3B were discovered in only nine of our 14 ICF patients. Moreover, two ICF patients from consanguineous families who did not show autozygosity (i.e. homozygosity by descent) for the DNMT3B locus did not reveal DNMT3B mutations, suggesting genetic heterogeneity for this disease. Mutation analysis revealed 11 different mutations, including seven novel ones: eight different missense mutations, two different nonsense mutations, and a splice-site mutation leading to the insertion of three aa's. The missense mutations occurred in or near the catalytic domain of DNMT3B protein, indicating a possible interference with the normal functioning of the enzyme. However, none of the ICF patients was homozygous for a nonsense allele, suggesting that absence of this enzyme is not compatible with life. Compound heterozygosity for a missense and a nonsense mutation did not seem to correlate with a more severe phenotype.

Abnormalities, Multiple↗

PubMed2006

A two-tier approach to mutation detection in the COL4A5 gene for Alport syndrome.

About 85% of Alport syndrome is an X-linked semi-dominant condition caused by mutations in the collagen gene, COL4A5. The large size and high GC content of this gene have presented diagnostic laboratories with problems in identifying mutations with greater than about a 50% success rate since the gene was first cloned 16 years ago. An RNA based approach is adopted here for a first pass mutation scanning coupled with more traditional exon-by-exon screening to increase the rate of mutation identification. Twenty-one mutations were identified in twenty-five patients with clear Alport syndrome including four gross deletions, two deep intronic mutations, three frameshifts, three splice site mutations, eight missense mutations and one inframe deletion.

Base Sequence↗

PubMed1995

The molecular genetic basis of myophosphorylase deficiency (McArdle's disease).

Glycogen phosphorylase catalyzes the first step of glycogen catabolism. Hereditary defects of muscle phosphorylase lead to a myopathy characterized by exercise intolerance, cramps, and myoglobinuria (McArdle's disease). We have identified ten mutations in the myophosphorylase gene in patients with McArdle's disease. Relatively common mutations include: a nonsense mutation, CGA(Arg) to TGA at codon 49, observed in 30 of 40 American patients; deletion of a single codon 708/709, observed in 4 of 7 Japanese patients; and a missense mutation, GGC(Gly) to AGC(Ser) at codon 204, observed in 5 of 40 American patients. Apparently rare mutations include: a splice-junction mutation, G to A, at the first nt of intron 14; a deletion of G at codon 510; a mutation, ATG to CTG, in the translation initiation codon; and missense mutations, AAG(Lys) to ACG(Thr) at codon 542, CTG(Leu) to CCG(Pro) at codon 396, CTG(Leu) to CCG(Pro) at codon 291, and GAG(Glu) to AAG(Lys) at codon 654. As most mutations can be screened for using genomic DNA, patients can now be diagnosed reliably using peripheral blood cells, thus avoiding muscle biopsy. Although these findings define the wide spectrum of genetic lesions causing McArdle's disease, the clinical heterogeneity of this disorder remains to be explained.

Base Sequence↗

PubMed1995

Molecular genetic heterogeneity of phosphoglycerate kinase (PGK) deficiency.

Phosphoglycerate kinase (PGK; EC 2.7.2.3) is a glycolytic enzyme encoded by a single gene on the X chromosome and ubiquitously expressed. Hereditary PGK deficiency can cause hemolytic anemia, central nervous system dysfunction, and/or myopathy characterized by exercise intolerance, cramps, and myoglobinuria. So far, 20 PGK variants with reduced PGK activity have been identified, 8 of them in patients with myopathy. Six missense mutations and one splice-junction mutation have been identified in 7 patients, 2 of whom had myopathy. However, the biochemical and molecular bases for clinical heterogeneity in PGK deficiency remain unknown.

Base Sequence↗

PubMed1992

Molecular aspects of Alport's syndrome.

We review the recent progress achieved on the understanding of the molecular basis of Alport's syndrome. This inherited disease is defined as progressive nephritis with sensorineural hearing loss. In 80%-85% of the families, inheritance is compatible with X-linked dominant transmission, whereas in the remaining cases autosomal dominant transmission is assumed. Histology studies demonstrated that the main defect is within the glomerular basement membrane (GBM). In addition, evidence for an altered GBM antigenicity came from immunofluorescence studies which showed a reduced or absent binding of anti-GBM autoantibodies or monoclonal antibodies to the "Goodpasture antigen" in some families. Subsequent studies added substantial evidence that Alport's syndrome is a type IV collagen disease. Genetic linkage analyses coherently identified an Alport locus at the X-chromosomal region Xq21.3-22. Recently, a previously unknown alpha 5 chain of type IV collagen was identified, and the corresponding gene was also mapped to Xq22. Subsequent studies on Alport families by various groups identified more than 25 COL4A5 lesions. Segregation in linkage with the Alport phenotype could be shown in large kindreds. Mainly deletions and only a few point mutations were described. Most lesions reported so far are heterogeneous. We were able to identify two deletions and one point mutation involving a 3' splice site in 20 Alport families from Germany. One of the patients with a COL4A5 deletion and the patient with the splice site mutation developed anti-GBM antibodies after renal transplantation. In contrast, no COL4A5 lesions have been found in 2 further patients with posttransplant anti-GBM nephritis.(ABSTRACT TRUNCATED AT 250 WORDS)

Basement Membrane↗

PubMed2006

Optineurin gene is not involved in the common high-tension form of primary open-angle glaucoma.

PURPOSE: To assess the influence of optineurin in the more common high-tension, primary open-angle glaucoma (POAG). METHODS: Eighteen sporadic cases and 35 probands from 35 familial cases, including three families with one member having normal-tension glaucoma (NTG), were enrolled. Using transgenomic WAVE denaturing high-performance liquid chromatography (DHPLC), all coding portion of the optineurin gene (from exon 4 to exon 16) was analyzed. Samples displaying an altered elution profile were sequenced to confirm and identify sequence variants. Exon 4 containing the previously reported p.E50K (Glu50Lys) recurrent mutation (covering 13% of normotensive cases) was entirely sequenced. RESULTS: We did not detect the mutation p.E50K, and we did not find any other pathogenic mutation. A putative splice-site mutation was detected in one family. Extension of segregation analysis to additional family members and mRNA investigation failed to establish a certain involvement of this mutation with the disease. We detected a number of common polymorphisms, including the previously reported p.M98K (Met98Lys) variant. CONCLUSIONS: In this population, mutations in the optineurin gene are not associated with adult-onset primary POAG.

Adult↗

PubMed1999

Mutations in JAGGED1 gene are predominantly sporadic in Alagille syndrome.

BACKGROUNDS & AIMS: Mutations in the JAGGED1 gene are responsible for the Alagille syndrome, an autosomal dominant disorder characterized by neonatal jaundice, intrahepatic cholestasis, and developmental disorders affecting the liver, heart, vertebrae, eyes, and face. We screened a large group of patients for mutations in JAGGED1 and studied transmission of the mutations. METHODS: The coding sequence of the JAGGED1 gene was searched by single-strand conformation polymorphism and sequence analysis for mutations in 109 unrelated patients with the Alagille syndrome and their family if available. RESULTS: Sixty-nine patients (63%) had intragenic mutations, including 14 nonsense mutations, 31 frameshifts, 11 splice site mutations, and 13 missense mutations. We identified 59 different types of mutation of which 54 were previously undescribed; 8 were observed more than once. Mutations were de novo in 40 of 57 probands. CONCLUSIONS: Most of the observed mutations other than the missense mutations in JAGGED1 are expected to give rise to truncated and unanchored proteins. All mutations mapped to the extracellular domain of the protein, and there appeared to be regional hot spots, although no clustering was observed. Thus, the sequencing of 7 exons of JAGGED1 would detect 51% of the mutations. Transmission analysis showed a high frequency of sporadic cases (70%).

Alagille Syndrome↗