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Results for “Splicing mutations”

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At least 451 records · Page 25Linked to original sources

PubMed2001

Identification of the first reported splice site mutation (IVS7-1G-->A) in the aminomethyltransferase (T-protein) gene (AMT) of the glycine cleavage complex in 3 unrelated families with nonketotic hyperglycinemia.

A novel splice site mutation (IVS7-1G-->A) in the T-protein gene (aminomethyltransferase, or AMT) of the glycine cleavage enzyme complex was found in a patient with nonketotic hyperglycinemia (NKH). A PCR/restriction enzyme method to detect this mutation was used to screen 100 NKH alleles and identified the mutation in three unrelated families.

Amino Acid Oxidoreductases↗

PubMed1993

An IVS-I-117 (G-->A) acceptor splice site mutation in the alpha 1-globin gene is a nondeletional alpha-thalassaemia-2 determinant in an Indian population.

In 1991 we reported the identification of two deletional alpha-thalassaemia-2 determinants (-3.7 kb and -4.2 kb) and one nondeletional alpha-thalassaemia-2 determinant (Hb Koya Dora alpha 2 codon 142, TAA-->TCA) in a tribal population in Central India (Gupta et al, 1991). Evidence was obtained at that time for the possible presence of an additional nondeletional alpha-thalassaemia-2 because of low levels of Hb S (< 28%) in some Hb S heterozygotes with a simple alpha-thalassaemia-2 heterozygosity (-alpha/alpha alpha). This abnormality has now been identified as a G-->A mutation at IVS-I-117 of the alpha 1-globin gene (acceptor splice site) which makes this gene nonfunctional. Its frequency was established at approximately 6% which raises the total frequency of alpha-thalassaemia determinants in this population to approximately 60%. Subjects with a deletional alpha-thalassaemia-2 and the newly discovered alpha 1 acceptor splice junction mutation in trans appear to have an alpha chain deficiency similar to that of an alpha-thalassaemia-2 homozygote (-alpha/-alpha). An additional change (C-->G) at the Cap -4 site was observed in six alpha 1- and one alpha 2-globin genes; this polymorphism is not associated with a decrease in alpha chain synthesis and is not linked to the IVS-I-117 (G-->A) mutation.

Adolescent↗

PubMed2003

46,XY phenotypic male with focal segmental glomerulosclerosis caused by the WT1 splice site mutation.

OBJECTIVE: Frasier syndrome is characterized by progressive glomerulopathy due to nonspecific focal and segmental glomerulosclerosis (FSGS), 46,XY sex reversal and the development of gonadoblastoma from dysgenetic gonads. Donor splice site heterozygous mutations in intron 9 of the Wilms' tumor gene (WT1) cause this disease. We investigated whether WT1 mutations showed clinical heterogeneity. PATIENTS AND METHODS: A 6-year-old phenotypic boy was diagnosed as having FSGS. His karyotype was 46,XY. Gonadotropin-releasing hormone and human chorionic gonadotropin stimulation tests revealed normal luteinizing hormone, follicle-stimulating hormone and testosterone responses. The other patient was a 7-year-old 46,XY female with FSGS. Prophylactic gonadectomy was performed and gonadoblastoma was found. By polymerase chain reaction and direct sequencing, WT1 was analyzed in these patients. RESULTS AND CONCLUSION: Both patients had IVS9 + 5G-->A in intron 9 of the WT1. Our study indicates a normal 46,XY phenotypic male patient with FSGS. The phenotypic variations of the WT1 splice site mutations are further expanded.

Child↗

PubMed1998

Characterization of the gene encoding the human Kidd blood group/urea transporter protein. Evidence for splice site mutations in Jknull individuals.

The Kidd (JK) blood group is carried by an integral membrane glycoprotein which transports urea through the red cell membrane and is also present on endothelial cells of the vasa recta in the kidney. The exon-intron structure of the human blood group Kidd/urea transporter gene has been determined. It is organized into 11 exons distributed over 30 kilobase pairs. The mature protein is encoded by exons 4-11. The transcription initiation site was identified by 5'-rapid amplification of cDNA ends-polymerase chain reaction at 335 base pairs upstream of the translation start point located in exon 4. The 5'-flanking region, from nucleotide -837 to -336, contains TATA and inverted CAAT boxes as well as GATA-1/SP1 erythroid-specific cis-acting regulatory elements. Analysis of the 3'-untranslated region reveals that the two equally abundant erythroid transcripts of 4.4 and 2.0 kilobase pairs arise from usage of different alternative polyadenylation signals. No obvious abnormality of the Kidd/urea transporter gene, including the 5'- and 3'-untranslated regions, has been detected by Southern blot analysis of the blood of two unrelated Jknull individuals (B.S. and L.P.), which lacks all Jk antigens and Jk proteins on red cells, but was genotyped as homozygous for a "silent" Jkb allele. Further analysis indicated that different splice site mutations occurred in each variant. The first mutation affected the invariant G residue of the 3'-acceptor splice site of intron 5 (variant B.S.), while the second mutation affected the invariant G residue of the 5'-donor splice site of intron 7 (variant L.P.). These mutations caused the skipping of exon 6 and 7, respectively, as seen by sequence analysis of the Jk transcripts present in reticulocytes. Expression studies in Xenopus oocytes demonstrated that the truncated proteins encoded by the spliced transcripts did not mediate a facilitated urea transport compared with the wild type Kidd/urea transporter protein and were not expressed on the oocyte's plasma membrane. These findings provide a rational explanation for the lack of Kidd/urea transporter protein and defect in urea transport of Jknull cells.

Base Sequence↗

PubMed2004

An unusual arylsulfatase A pseudodeficiency allele carrying a splice site mutation in a metachromatic leukodystrophy patient.

A late infantile metachromatic leukodystrophy patient was found to be heterozygous for the arylsulfatase A (ARSA) pseudodeficiency (pd) polyadenylation site variant ((*)96A>G) in the absence of the commonly associated N-glycosylation site variant (N350S). ARSA alleles were sequenced and the genotype completely defined. Six sequence variations were identified, among which two resulted as severe disease-causing mutations, both leading to the loss of the reading frame: a splice acceptor site mutation in intron 4 (849-1G>A), located on the (*)96A>G allele and a mononucleotide deletion (258delC) in exon 2, located on the other allele. The altered splicing caused by the 849-1G>A mutation was shown by in vitro expression of a recombinant gene containing the genomic region surrounding the mutation. Haplotype analysis of the unusual pd allele was performed in order to investigate its possible origin.

Alleles↗

PubMed2004

Identification of a novel EYA1 splice-site mutation in a Danish branchio-oto-renal syndrome family.

Branchio-oto-renal (BOR) syndrome is an autosomal dominant disorder characterized by variable clinical manifestations including branchial fistulae, preauricular pits, ear malformations, hearing impairment, and renal anomalies. BOR is caused by mutations in the genes EYA1 and SIX1. A Danish BOR family with five affected individuals in three generations was analyzed for mutations in all 17 exons of EYA1 using direct sequencing of polymerase chain reaction (PCR) amplified genomic DNA. A novel splice-site mutation (IVS9+1 G>C) was detected in all affected family members but not in unaffected family members or in 96 controls. We conclude that this mutation is causing BOR in the family, most likely as a result of haploinsufficiency or an abnormal protein product caused by aberrant splicing of EYA1 mRNA.

Branchio-Oto-Renal Syndrome↗

PubMed1998

Analysis of Four Common Salt-Wasting Mutations in CYP21 (Steroid 21-Hydroxylase) by Cleavase Fragment Length Polymorphism Analysis and Characterization of a Frequent Polymorphism in Intron 6.

Background: Congenital adrenal hyperplasia (CAH) owing to steroid 21-hydroxylase deficiency results from mutations in CYP21. The majority of patients with this disorder have salt-wasting because of mineralocorticoid deficiency, and most patients with salt-wasting have one of four common mutations: deletions of CYP21, or nondeletion mutations including a 3 < 9 premature splice mutation in intron 2; an 8-bp deletion in exon III; a cluster of mutations in exon VI; and R356W. Methods and Results: The authors analyzed these mutations using a new mutation-detection methodology, cleavase fragment length polymorphism (CFLP) analysis. All of these mutations were detectable using CFLP. The intron 2 splice mutation, exon III 8-bp deletion, and R356W mutation all resulted in novel CFLP bands not seen in subjects without those mutations. The exon VI cluster of mutations resulted in elimination of a CFLP band, which was easily detected in a patient with that mutation and a gene deletion on the homologous chromosome. The authors also report the characterization of a restriction fragment length polymorphism in intron 6 involving the RsaI site around nucleotide 1419. In 48 chromosomes from the parental generation of the Centre d'Étude du Polymorphisme Humain families, the frequency of the polymorphism that destroys the RsaI site was found to be 12.5%. Conclusions: CFLP is a potentially useful analytic method for analyzing frequent CYP21 mutations that cause salt-wasting CAH, although further development of the technique is required to clearly distinguish heterozygotes from homozygotes for mutations that generate novel CFLP bands and to identify heterozygotes for mutations that eliminate a CFLP band. The Rsa I polymorphism may be a useful marker for following the segregation of CYP21 alleles in genetic studies and is of use in showing gene deletions of CYP21 in informative families. The polymorphism may also be of use in genetic studies of the human major histocompatibility complex.

Journal Article↗

PubMed1998

Type 2 Gaucher disease with hydrops fetalis in an Ashkenazi Jewish family resulting from a novel recombinant allele and a rare splice junction mutation in the glucocerebrosidase locus.

Gaucher disease, the deficiency of the lysosomal enzyme glucocerebrosidase (EC 3.2.1.45), is frequently encountered in the Ashkenazi Jewish population. Carrier screening for Gaucher disease by enzyme analysis performed during a routine pregnancy indicated that both Ashkenazi parents were carriers. Screening for four common Gaucher mutations was subsequently performed on fetal and parental DNA. None of the common Ashkenazi mutations were identified. However, when exons 9-11 were amplified and digested with NciI to detect the L444P mutation, it appeared that the mother and the fetus had an unusual allele and that the expected paternal allele was not present. When the fetal amniocytes were found to have less than 2% of the normal glucocerebrosidase activity and a fetal sonogram revealed hydrops fetalis, the pregnancy was terminated. The diagnosis of severe type 2 Gaucher disease was confirmed at autopsy. Ultrastructural studies of epidermis from the fetus revealed the characteristic disruption of lamellar bilayers, diagnostic for type 2 Gaucher disease. In subsequent studies of the fetal DNA, long-template polymerase chain reaction amplification revealed one appropriately sized band (approximately 6.5 kb) and one smaller (approximately 5.2 kb) band. Sequencing of the approximately 5.2-kb fragment identified a novel fusion allele resulting from recombination between the glucocerebrosidase gene and its pseudogene beginning in intron 3. This fusion allele was inherited from the father. The result was confirmed by Southern blot analysis using the enzyme S8tII. Sequencing of the 6.5-kb fragment identified a previously described, although rare, T-to-G splice junction mutation in intron 10 of the maternal allele, which introduced an NciI site. The couple had a subsequent pregnancy which was also found to be affected. This case study identifies a novel recombinant allele and an unusual splice junction mutation, and demonstrates that even in the Ashkenazi population, screening for common mutations may not accurately identify the most severe forms of the disease.

Alleles↗

PubMed1993

Identification of a splice-site mutation in the low density lipoprotein receptor gene by denaturing gradient gel electrophoresis.

We have applied the denaturing gradient gel electrophoresis (DGGE) technique to detect sequence variations in exon 9 of the low density lipoprotein receptor (LDLR) gene in individuals with heterozygous familial hypercholesterolemia (FH). A fragment containing exon 9 and 25 base pairs (bp) of the intron boundary sequence at either side was amplified. To this fragment a 40-bp GC-clamp was attached by the polymerase chain reaction (PCR). We have analyzed a total of 165 DNA samples of FH patients and have detected a mutation in three cases. Two patients were found to have the previously described "South African" G to A transition in codon 408. In a third patient, we observed a different banding pattern of the DNA fragments on DGGE indicating a different mutation. The mutant homoduplex band of this sample was purified from the gel, cloned in an AT-vector and sequenced. Sequence analysis demonstrated a G to A transition of the consensus G-nucleotide at the intron 9 splice donor site. Cosegregation between this mutation and elevated plasma cholesterol levels was observed in family members of this FH patient. This mutation probably prevents normal splicing of the mRNA and represents the first identified splice-site mutation in the LDLR gene. We conclude that the use of DGGE of GC-clamped PCR-amplified exon sequences offers a general strategy for the detection of disease-producing mutations in the LDLR gene.

Base Sequence↗

PubMed2004

Cerebrotendinous xanthomatosis in a Hong Kong Chinese kinship with a novel splicing site mutation IVS6-1G>T in the sterol 27-hydroxylase gene.

We reported a Hong Kong Chinese proband with Cerebrotendinous Xanthomatosis in which a novel acceptor splicing site mutation (IVS6-1G>T) was identified. Family screening revealed the same mutation in his elder brother and the youngest sister. All the three affected siblings were compound heterozygous for IVS6-1G>T and a known missense mutation R372Q (GenBank Accession No. M62401). Significant phenotypic variation was noted among them that the youngest sister was still symptom-free at the time of writing.

Asian People↗

PubMed2000

Novel splice site mutation of aspartoacylase gene in a Turkish patient with Canavan disease.

Canavan disease is a severe, progressive autosomal recessive neurodegenerative leukodystrophy. Canavan disease occurs more frequently among Ashkenazi Jewish individuals with two predominant mutations in the aspartoacylase (ASPA) gene. The disease is less frequent in non-Jewish individuals and the mutations randomly reside on the ASPA gene, with one mutation seen more frequently among patients of European extraction. In the present study we report a novel homozygous donor splice site mutation of intron 4 in a child with first-cousin parents of Turkish extraction.

Amidohydrolases↗

PubMed1998

Glanzmann thrombasthenia in two Iraqi-Jewish siblings is caused by a novel splice junction mutation in the glycoprotein IIb.

An A-->G transition in the acceptor splice site at the intron 19/exon 20 junction of the glycoprotein IIb gene was defined as a novel mutation causing Glanzmann thrombasthenia in two Iraqi-Jewish siblings. This mutant DNA was transcribed into four distinct species of mRNA, one of which resulted in a premature termination codon and the other three predicting deletions of 50, 61 or 72 amino acids, respectively.

Aged↗

PubMed1986

A compensatory base change in U1 snRNA suppresses a 5' splice site mutation.

Indirect evidence suggests that the 5' end of U1 snRNA recognizes the 5' splice site in mRNA precursors by complementary base pairing. To test this hypothesis, we asked whether point mutations in the alternative 12S and 13S 5' splice sites of the adenovirus E1A gene can be suppressed by compensatory base changes in human U1 snRNA. When the mutant E1A and U1 genes are contransfected into HeLa cells, we observe efficient suppression of one mutation at position +5 in the 12S splice site, but exceedingly weak suppression of another mutation at position +3 in the 13S splice site. These and other results suggest that base pairing between U1 and the 5' splice site is necessary but not sufficient for the splicing of mRNA precursors.

Adenoviruses, Human↗

PubMed1999

Splice-site mutation in the PDS gene may result in intrafamilial variability for deafness in Pendred syndrome.

Pendred syndrome is a recessive inherited disorder that consists of developmental abnormalities of the cochlea, sensorineural hearing loss, and diffuse thyroid enlargement (goiter). This disorder may account for up to 10% of cases of hereditary deafness. The disease gene (PDS) has been mapped to chromosome 7q22-q31, and encodes a chloride-iodide transport protein. We performed mutation analysis of individual exons of the PDS gene in one Spanish family that shows intrafamilial variability of the deafness phenotype (two patients with profound and one with moderate-severe deafness). We identified a new splice-site mutation affecting intron 4 of the PDS gene, at nucleotide position 639+7. RNA analysis from lymphocytes of the affected patients showed that mutation 639+7A-->G generates a new donor splice site, leading to an mRNA with an insertion of six nucleotides from intron 4 of PDS. Since the newly created donor splice site is likely to compete with the normal one, variations of the levels of normal and aberrant transcripts of the PDS gene in the cochlea may explain the variability in the deafness presentation.

Amino Acid Sequence↗

PubMed2000

Short stature in carriers of recessive mutation causing familial isolated growth hormone deficiency.

Isolated growth hormone deficiency (IGHD) IB is an autosomal recessive disorder characterized by a good response to exogenous growth hormone (GH) treatment without development of anti-GH antibodies. Patients with IGHD IB were found to be compound heterozygotes for deletion and frameshift mutations as well as homozygotes for splicing mutations in the GH-1 gene. Recently, a novel splicing mutation in the GH-1 gene was identified in an extended, consanguineous Arab-Bedouin family from Israel with IGHD IB. Prior to the identification of this mutation, a considerable number of children with short stature in this family were found normal on pharmacological stimulation for GH release. This observation prompted a genotype/phenotype correlation of potential heterozygotes in the family. Carriers of the mutant GH-1 allele were found as a group to have a significantly shorter stature than normal homozygote (mean standard deviation scores, 1.67 and -0.40, respectively, P<0.05). Moreover, 11 of 33 (33%) heterozygotes, but only 1 of 17 (5.9%) normal homozygotes, had their height at 2 or more SD below the mean. Overall, 48.5% of studied heterozygotes were found to be of appreciably short stature with height at or lower than the 5th centile (> or = -1.7 SD), whereas only 5.9% of the normal homozygotes did (P<0.004). This phenomenon of heterozygotes for a recessive mutation in the GH-1 gene manifesting short stature, might imply that some such mutations may account for non-GH deficiency reduced height in the general population.

Body Height↗

PubMed1999

Correction of aberrant splicing of the cystic fibrosis transmembrane conductance regulator (CFTR) gene by antisense oligonucleotides.

The CFTR splicing mutation 3849 + 10 kb C --> T creates a novel donor site 10 kilobases (kb) into intron 19 of the gene and is one of the more common splicing mutations that causes cystic fibrosis (CF). It has an elevated prevalence among patients with atypically mild disease and normal sweat electrolytes and is especially prominent in Ashkenazi Jews. This class of splicing mutations, reported in several genes, involves novel splice sites activated deep within introns while leaving wild-type splice elements intact. CFTR cDNA constructs that modeled the 3849 + 10 kb C --> T mutation were expressed in 3T3 mouse fibroblasts and in CFT1 human tracheal and C127 mouse mammary epithelial cells. In all three cell types, aberrant splicing of CFTR pre-mRNA was comparable to that reported in vivo in CF patients. Treatment of the cells with 2'-O-methyl phosphorothioate oligoribonucleotides antisense toward the aberrant donor and acceptor splice sites or to the retained exon-like sequence, disfavored aberrant splicing and enhanced normal processing of CFTR pre-mRNA. This antisense-mediated correction of splicing was dose- and sequence-dependent and was accompanied by increased production of CFTR protein that was appropriately glycosylated. Antisense-mediated correction of splicing in a mutation-specific context represents a potential gene therapy modality with applicability to many inherited disorders.

3T3 Cells↗

PubMed1998

Molecular basis for the dominant white phenotype in the domestic pig.

The change of phenotypic traits in domestic animals and crops as a response to selective breeding mimics the much slower evolutionary change in natural populations. Here, we describe that the dominant white phenotype in domestic pigs is caused by two mutations in the KIT gene encoding the mast/stem cell growth factor receptor (MGF), one gene duplication associated with a partially dominant phenotype and a splice mutation in one of the copies leading to the fully dominant allele. The splice mutation is a G to A substitution in the first nucleotide of intron 17 and leads to skipping of exon 17. The duplication is most likely a regulatory mutation affecting KIT expression, whereas the splice mutation is expected to cause a receptor with impaired or absent tyrosine kinase activity. Immunocytochemistry showed that this variant form is expressed in 17- to 19-day-old pig embryos. Hundreds of millions of white pigs around the world are assumed to be heterozygous or homozygous for the two mutations. [The EMBL accession numbers for porcine KIT1*0101, KIT1*0202, KIT2*0202, and KIT2*0101 are AJ223228-AJ223231, respectively.]

Alternative Splicing↗

PubMed2004

Insulin-like growth factor (IGF) parameters and tools for efficacy: the IGF-I generation test in children.

Serum levels of growth hormone (GH)-dependent peptides could provide important and valuable measures of GH sensitivity and, potentially, responsiveness. In normal individuals, serum insulin-like growth factor I (IGF-I) concentrations are dependent on the dose of GH given, with IGF-I responsiveness not decreasing with age. Individuals heterozygous for the E180 GH receptor (GHR) splice mutation have normal IGF-I generation, but those homozygous for the E180 splice mutation have very low basal and stimulated IGF-I concentrations. Similar results are observed for the serum IGF-binding protein 3 (IGFBP-3) response to GH, with a correlation between changes in serum concentrations of IGF-I and changes in IGFBP-3 in normal, heterozygotic, GH-insensitive and GH-deficient participants. In individuals with the E180 splice mutation, IGF-I and IGFBP-3 tests show sensitivity and specificity for detecting GH insensitivity (GHI). In children with idiopathic short stature, it appears that some individuals have selective resistance to GH, with their ability to generate IGF-I more impaired than their ability to generate other GH-dependent peptides. This heterogeneous group may require individualization of GH dosage. IGF generation tests remain the best short-term, in vivo test for classic GHI, although diagnostic tests will undoubtedly require further modification to identify milder pathophysiologic abnormalities.

Adolescent↗