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PubMed2006

Maternal origin of a novel C-terminal truncation mutation in CDKL5 causing a severe atypical form of Rett syndrome.

The CDKL5 gene has been implicated in infantile spasms and more recently in a Rett syndrome-like phenotype. We report a case of a young girl presenting generalized convulsions at 10 days of life. Subsequent mutation analysis by denaturing high-performance liquid chromatography of MECP2 and CDKL5 genes revealed heterozygosity for a c.47_48insAGG insertion in exon 1 of MECP2 and heterozygosity for a new nonsense mutation p.Q834X and a new missense variant p.V999M in the CDKL5 gene. Co-segregation analysis showed that the nonsense mutation was a de novo mutation and that the insertion and the missense variant were also found in the asymptomatic mother. In the absence of skewed X inactivation in the mother, it is likely that these last two variants are not pathogenic. Reverse transcription-polymerase chain reaction from lymphoblastoid cells of the patient showed only the transcript without the nonsense and missense variations suggesting decreased stability of mature mRNA by nonsense-mediated decay. These data also suggest an occurrence of the de novo mutation in maternal germ line cells. Moreover, this report reinforces the observation that the CDKL5 phenotype overlaps with Rett syndrome and that CDKL5 gene analysis is recommended in females with a seizure disorder commencing in the first weeks of life.

Base Sequence↗
PubMed2002

Clinically relevant aminoglycosides can suppress disease-associated premature stop mutations in the IDUA and P53 cDNAs in a mammalian translation system.

Recent studies have suggested that the use of aminoglycosides to suppress disease-causing nonsense mutations may be a promising new therapy for a large number of genetic diseases. However, gentamicin is currently the only clinically relevant aminoglycoside shown to suppress premature stop mutations in a mammalian system. We compared the ability of the clinically approved aminoglycosides gentamicin, tobramycin, and amikacin to suppress premature stop mutations. Using readthrough reporter constructs as well as mammalian cDNAs containing naturally occurring premature stop mutations, we found that each of these aminoglycosides can suppress many premature stop mutations in a context-dependent manner in a mammalian translation system. Our results indicate that the tetranucleotide termination signal (the stop codon and the nucleotide 3' of the stop codon) is the primary determinant for aminoglycoside-mediated suppression. The levels of termination suppression achieved by tobramycin were substantially lower than those observed with gentamicin. In contrast, amikacin stimulated suppression in a manner that was generally similar to gentamicin. Amikacin produced higher levels of readthrough than gentamicin at some contexts, demonstrating a unique pattern of context dependence. Experiments with mammalian cDNAs confirmed these results and demonstrated that these aminoglycosides can also suppress disease-associated premature stop mutations previously identified in the IDUA gene (responsible for the lysosomal storage disease mucopolysaccharidosis I) and the P53 gene (associated with many forms of cancer). Taken together, these results suggest that amikacin represents an alternative to gentamicin for suppression therapy in certain contexts, thus providing a means of optimizing the efficacy of aminoglycoside-mediated suppression of premature stop mutations.

Amikacin↗
PubMed2003

Epidermolysis bullosa simplex in Israel: clinical and genetic features.

BACKGROUND: Epidermolysis bullosa simplex (EBS) is the most common form of epidermolysis bullosa. The disease is characterized by intraepidermal blistering due in most cases to mutations in cytokeratin genes 5 (K5) or 14 (K14). Extensive studies in the United States and Europe have shown that EBS is almost always inherited in an autosomal dominant fashion. OBJECTIVE: To assess the possibility that the molecular features of EBS may differ according to the type of population studied. DESIGN: We assessed 10 Israeli families diagnosed as having EBS and compared their clinical and genetic features with previous observations. Affected individuals underwent complete clinical evaluation. DNA from all family members was assessed for mutations in K5 or K14 using polymerase chain reaction amplification, direct sequencing, and subsequent mutation verification. In addition, specific cases were genotyped using a panel of microsatellite markers spanning the K14 locus. RESULTS: Eight distinct pathogenic mutations in K5 (3 mutations) and K14 (5 mutations) were identified. Six of these mutations are novel. The mutations included 2 nonsense mutations and 6 missense mutations. A third of the affected families inherited EBS in a recessive fashion, in contrast with previous observations in Europe and the United States. In addition, we identified a unique case that resulted from compound heterozygosity for a missense and a nonsense mutation in K14. Homozygous nonsense mutations were strongly associated with a severe phenotype. CONCLUSION: The present study demonstrates a unique mutation spectrum and a strikingly different pattern of inheritance for EBS in a series of Israeli families compared with families of European or US extraction.

Codon, Nonsense↗
PubMed2002

Genetic analysis of patients with leukocyte adhesion deficiency: genomic sequencing reveals otherwise undetectable mutations.

OBJECTIVE: The aim of this study was to analyze mutations in DNA from patients with leukocyte adhesion deficiency (LAD), an immunodeficiency caused by absence of the beta(2) subunit (CD18) of the leukocyte integrins LFA-1 (CD11a/CD18), Mac-1 (CD11b/CD18), p150,95 (CD11c/CD18), and CR4 (CD11d/CD18). METHODS: We developed genomic DNA PCR sequencing to detect mutations not only in exons but also in introns. RESULTS: Eight LAD patients were analyzed, of which five had homozygous mutations, i.e., a 0.8-kb deletion, a branchpoint mutation in intron 5 causing mRNA missplicing, a nonsense mutation, and two missense mutations. Four of these mutations are novel. We cotransfected the two mutant CD18 proteins with normal CD11a, b, or c in COS cells. This resulted in absence of all three beta(2) integrins on the surface of cells transfected with CD18(252Arg). However, CD18(593Cys) supported some LFA-1 and p150,95 formation in COS cells. The other three patients were compound heterozygotes in which only one allele had previously been characterized, because the other alleles were undetectable at the cDNA level. We identified the unknown mutations as a novel two-nucleotide deletion, a nonsense mutation, and a single nucleotide deletion. CONCLUSION: Our method allows identification of mutations in CD18 from genomic DNA. This opens the possibility of early prenatal diagnosis of LAD and reliable carrier detection.

Alleles↗
PubMedDate not supplied

Can mucopolysaccharidosis type I disease severity be predicted based on a patient's genotype? A comprehensive review of the literature.

Mucopolysaccharidosis type I (MPS I) is an autosomal recessive genetic disorder that results in a wide range of clinical symptoms from mild somatic complications and a normal lifespan to severe central nervous system involvement and a significantly shortened lifespan. An extensive review of the literature was performed to pool data from studies that have identified mutations in patients with mucopolysaccharidosis type I (MPS I) and have reported clinical information about disease severity in an attempt to make correlations between a patient's genotype and phenotype. To date, all patients with a nonsense mutation identified on both alleles have developed the severe form of MPS I. The phenotypes of patients with missense, insertion, deletion, or splice site mutations are much more variable. Missense mutations are the most likely to allow for some residual enzyme activity, and in particular, the R89Q mutation has been identified in several mild patients even when in combination with a nonsense mutation. Conversely, most splice site and insertion/deletion mutations result in the severe phenotype unless in combination with a less severe missense mutation. Currently, genotype-phenotype correlations cannot be confidently made unless the patient has 2 nonsense mutations. Although most families have private mutations, some insight into phenotypic expression may be obtained by observing the clinical severity of other patients with the same genotype. This review also confirms that MPS I allele frequencies vary between different ethnic populations, and that W402X and Q70X are the most common mutations and are present in over 50% of Caucasian alleles.

Alleles↗
PubMedDate not supplied

Variety of nonsense suppressor phenotypes associated with mutational changes at conserved sites in Escherichia coli ribosomal RNA.

To screen for ribosomal RNA mutants defective in peptide chain termination, we have been looking for rRNA mutants that exhibit different patterns of suppression of nonsense mutations and that do not suppress missense mutations at the same positions in the same reporter gene. The rRNA mutations were induced by segment-directed randomly mutagenic PCR treatment of a cloned rrnB operon, followed by subcloning of the mutagenesis products and transformation of strains containing different nonsense mutations in the Escherichia coli trpA gene. To date, we have repeatedly obtained only two small sets of mutations, one in the 3' domain of 16S rRNA, at five nucleotides out of the 610 mutagenized (two in helix 34 and three in helix 44), and the other in 23S rRNA at only four neighboring nucleotide positions (in a highly conserved hexanucleotide loop) within the 1.4 kb mutagenized segment. There is variety, however, in the suppression patterns of the mutants, ranging from suppression of UAG or UGA, through suppression of UAG and UGA, but not UAA, to suppression of all three termination codons. The two helices in 16S rRNA have previously been associated both physically and functionally with the decoding center of the ribosome. The 23S region is part of the binding site for the large subunit protein L11 and the antibiotic thiostrepton, both of which have been shown to affect peptide chain termination. Finally, we have demonstrated that the 23S mutant A1093, which suppresses trpA UGA mutations very efficiently, is lethal at temperatures above 36 degrees C (when highly expressed). This lethality is overcome by secondary 23S rRNA mutations in domain V. Our results suggest that specific regions of 16S and 23S rRNA are involved in peptide chain termination, that the lethality of A1093 is caused by high-level UGA suppression, and that intramolecular interaction between domains II and V of 23S rRNA may play a role in peptide chain termination at the UGA stop codon.

Codon, Nonsense↗
PubMed2005

The facio-audio-symphalangism syndrome in a four generation family with a nonsense mutation in the NOG-gene.

We report a four generation family with features of the facio-audio-symphalangism syndrome. This condition is characterized by proximal symphalangism, conductive hearing loss due to stapes fixation and a distinctive facies. A novel nonsense mutation in the NOG gene on chromosome 17q22 was identified in the patients. The variable expression and progressive nature of the syndrome is well illustrated by this family. The role of Noggin as the causative factor of symphalangism is discussed.

Abnormalities, Multiple↗
PubMed2004

A nonsense mutation (E72X) in growth hormone releasing hormone receptor (GHRHR) gene is the major cause of familial isolated growth hormone deficiency in Western region of India: founder effect suggested by analysis of dinucleotide repeat polymorphism close to GHRHR gene.

An identical nonsense mutation (E72X) in growth hormone releasing hormone receptor (GHRHR) gene was identified in 17 patients with isolated GH deficiency belonging to one Muslim and four Hindu families residing in the Western part of India. Analysis of two dinucleotide repeat polymorphism, one at 6 kb downstream and the other at 13 kb downstream of GHRHR gene, revealed that all the patients shared the same homozygotic alleles at both loci. These results strongly indicate that the nonsense mutation occurred in a single ancestor and was subsequently transmitted to the descendants. This GHRHR mutation may be an important cause of familial IGHD in Western India and Sindh area of Pakistan as previous studies have also reported the same mutation.

Adolescent↗
PubMed2001

Ganglioside-induced differentiation-associated protein-1 is mutant in Charcot-Marie-Tooth disease type 4A/8q21.

We previously localized and fine-mapped Charcot Marie Tooth 4A (CMT4A), the autosomal recessive, demyelinating peripheral neuropathy, to chromosome 8. Through additional positional cloning, we have identified a good candidate gene, encoding ganglioside-induced differentiation-associated protein-1 (GDAP1). We found three different mutations in four different Tunisian families-two nonsense and one missense mutation. How mutations in GDAP1 lead to CMT4A remains to be understood.

Amino Acid Substitution↗
PubMed2000

PTCH gene mutations in odontogenic keratocysts.

An odontogenic keratocyst (OKC) is a benign cystic lesion of the jaws that occurs sporadically or in association with nevoid basal cell carcinoma syndrome (NBCCS). Recently, the gene for NBCCS was cloned and shown to be the human homologue of the Drosophila segment polarity gene Patched (PTCH), a tumor suppressor gene. The PTCH gene encodes a transmembrane protein that acts in opposition to the Hedgehog signaling protein, controlling cell fates, patterning, and growth in numerous tissues, including tooth. We investigated three cases of sporadic odontogenic keratocysts and three other cases associated with NBCCS, looking for mutations of the PTCH gene. Non-radioactive single-strand conformational polymorphism and direct sequencing of PCR products revealed a deletion of 5 base pairs (bp) in exon 3 (518delAAGCG) in one sporadic cyst as well as mutations in two cysts associated with NBCCS, a nonsense (C2760A) and a missense (G3499A) alteration. This report is the first to describe a somatic mutation of PTCH in sporadic odontogenic keratocysts as well as two novel mutations in cysts associated with NBCCS, indicating a similar pathogenesis in a subset of sporadic keratocysts.

Adult↗
PubMed2002

A nonsense mutation in exon 3 results in the HLA-B null allele B*5127N.

A new HLA-B null allele has been identified within the B*51 group by combined serological and molecular typing of an Italian Caucasoid family. Serological data indicated that the proband typed homozygous for A2 and B60. Confirmatory typing using sequence specific oligonucleotide hybridization (SSPOH) detected a second B allele within the B*51 group. Allele specific typing (SSP) for B*51 subtypes, including the known B*5111N allele, was performed, and typing results were consistent with B*5101, suggesting the presence of a new null variant. Cloning and sequencing of this allele identified a B*5101 variant with a nonsense mutation in exon 3. This new null allele has been designated B*5127N. The combined use of serologic and DNA-based typing methods facilitates the identification of null and low-expression alleles. An overview of null alleles of class I HLA is presented.

Base Sequence↗
PubMed2002

Listening to silence and understanding nonsense: exonic mutations that affect splicing.

Point mutations in the coding regions of genes are commonly assumed to exert their effects by altering single amino acids in the encoded proteins. However, there is increasing evidence that many human disease genes harbour exonic mutations that affect pre-mRNA splicing. Nonsense, missense and even translationally silent mutations can inactivate genes by inducing the splicing machinery to skip the mutant exons. Similarly, coding-region single-nucleotide polymorphisms might cause phenotypic variability by influencing splicing accuracy or efficiency. As the splicing mechanisms that depend on exonic signals are elucidated, new therapeutic approaches to treating certain genetic diseases can begin to be explored.

Codon, Nonsense↗
PubMed2003

[Identification of two novel factor XI non-sense mutation Trp228stop and Trp383stop in a Chinese pedigree of congenital factor XI deficiency].

OBJECTIVE: To identify the factor XI gene mutation in a Chinese pedigree of congenital factor XI deficiency. METHODS: The peripheral blood samples were collected from the proband and her family members and the plasma FXI:C and FXI:Ag were assayed. All the exons and their adjacent intron sequences of factor XI were amplified with PCR and sequenced thereafter. RESULTS: Two novel nonsense mutations TGG-->TGA (Trp228stop) and TGG-->TAG (Trp383stop) were identified in the family. CONCLUSION: The compound heterozygous Trp228stop and Trp383stop may attribute to the pathogenesis of the congenital factor deficiency.

Adult↗
PubMed2005

Low LDL cholesterol in individuals of African descent resulting from frequent nonsense mutations in PCSK9.

The low-density lipoprotein receptor (LDLR) prevents hypercholesterolemia and atherosclerosis by removing low-density lipoprotein (LDL) from circulation. Mutations in the genes encoding either LDLR or its ligand (APOB) cause severe hypercholesterolemia. Missense mutations in PCSK9, encoding a serine protease in the secretory pathway, also cause hypercholesterolemia. These mutations are probably gain-of-function mutations, as overexpression of PCSK9 in the liver of mice produces hypercholesterolemia by reducing LDLR number. To test whether loss-of-function mutations in PCSK9 have the opposite effect, we sequenced the coding region of PCSK9 in 128 subjects (50% African American) with low plasma levels of LDL and found two nonsense mutations (Y142X and C679X). These mutations were common in African Americans (combined frequency, 2%) but rare in European Americans (<0.1%) and were associated with a 40% reduction in plasma levels of LDL cholesterol. These data indicate that common sequence variations have large effects on plasma cholesterol levels in selected populations.

Adult↗
PubMed2004

Manipulation of nonsense mediated decay identifies gene mutations in colon cancer Cells with microsatellite instability.

Cancer cells showing microsatellite instability (MSI) demonstrate a high frequency of acquired frameshift mutations that result in the generation of nonsense mutations. RNA transcripts carrying these nonsense mutations are usually targeted for degradation through the nonsense mediated decay (NMD) pathway. Blocking this pathway with drugs such as emitine, results in the 'stabilization' of these mutant transcripts, which can now be detected on cDNA arrays. Unfortunately, emetine also induces a stress response that results in upregulation of additional transcripts which contribute to the analysis of the array. As a result, identifying which genes truly carry nonsense mutations is made more difficult. To overcome this, we have combined the emetine treatment with actinomycin D, which effectively prevents the upregulation of stress response genes while still stabilizing mutant transcripts. When we applied this modified approach to the analysis of MSI-positive colon cancer cells, we identified mutations in the UVRAG and p300 genes.

Cell Line, Tumor↗
PubMed2006

Nuclear suppression of mitochondrial defects in cells without the ND6 subunit.

Previously, we characterized a mouse cell line, 4A, carrying a mitochondrial DNA mutation in the subunit for respiratory complex I, NADH dehydrogenase, in the ND6 gene. This mutation abolished the complex I assembly and disrupted the respiratory function of complex I. We now report here that a galactose-resistant clone, 4AR, was isolated from the cells carrying the ND6 mutation. 4AR still contained the homoplasmic mutation, and apparently there was no ND6 protein synthesis, whereas the assembly of other complex I subunits into complex I was recovered. Furthermore, the respiratory activity and mitochondrial membrane potential were fully recovered. To investigate the genetic origin of this compensation, the mitochondrial DNA (mtDNA) from 4AR was transferred to a new nuclear background. The transmitochondrial lines failed to grow in galactose medium. We further transferred mtDNA with a nonsense mutation at the ND5 gene to the 4AR nuclear background, and a suppression for mitochondrial deficiency was observed. Our results suggest that change(s) in the expression of a certain nucleus-encoded factor(s) can compensate for the absence of the ND6 or ND5 subunit.

Animals↗
PubMed2006

A false note of DNA polymerase iota in the choir of genome caretakers in mammals.

DNA polymerase iota (Pol iota) of mammals is a member of the Y family of DNA polymerases. Among many other genome caretakers, these enzymes are responsible for maintaining genome stability. The members of the Y-family DNA polymerases take part in translesion DNA synthesis, bypassing some DNA lesions, and are characterized by low fidelity of DNA synthesis. A unique ability of Pol iota to predominantly incorporate G opposite T allowed us to identify the product of this enzyme among those synthesized by other DNA polymerases. This product can be called a "false note" of Pol iota. We measured the enzyme activity of Pol iota in crude extracts of cells from different organs of five inbred strains of mice (N3H/Sn, 101/H, C57BL/6, BALB/c, 129/J) that differed in a number of parameters. The "false note" of Pol iota was clearly sounding only in the extracts of testis and brain cells from four analyzed strains: N3H/Sn, 101/H, C57BL/6, BALB/c. In mice of 129/J strain that had a nonsense mutation in the second exon of the pol iota gene, the Pol iota activity was reliably detectable only in the extracts of brain. The data show that the active enzyme can be formed in some cell types even if they carry a nonsense mutation in the pol iota gene. This supports tissue-specific regulation of pol iota gene expression through alternative splicing. A semiquantitative determination of pol iota activity in mice strains different in their radiosensitivity suggests a reciprocal correlation between the enzyme activity of pol iota in testis and the resistance of mice to radiation.

Animals↗
PubMed2001

3-Hydroxy-3-methylglutaric aciduria in an Italian patient is caused by a new nonsense mutation in the HMGCL gene.

3-Hydroxy-3-methylglutaric aciduria is a rare autosomal recessive inborn error of metabolism caused by deficiency of the mitochondrial enzyme 3-hydroxy-3-methylglutaryl-CoA lyase (HMGCL). Up to now only a few mutations have been reported in the HMGCL gene. We report the first Italian patient, a female who presented metabolic acidosis at 3 days of age and then 3 months later. Analysis of urinary organic acids showed the excretion of 3-hydroxy-3-methylglutaric acid, 3-methylglutaconic acid, 3-methylglutaric acid, and 3-hydroxyisovaleric acid. A defect of HMGCL activity was suspected and then confirmed on cultured skin fibroblasts. Brain RM showed a diffuse mild abnormality of cerebral white matter in the periventricular regions, and the single voxel proton MRI spectroscopy showed abnormal peaks. In the patient's full-length HMGCL-cDNA a new c286C > T transition that leads to the stop codon Q96X was detected at the homozygous level. This mutation, that gives rise to a truncated protein, was confirmed in the patient's and also her parents' genomic DNA. The severe genetic lesion identified in the patient, which is in contrast with the mild clinical phenotype, stresses the importance of early diagnosis and therapy in HMGCL deficiency.

Brain↗