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PubMed2006

Missense mutations in the PCSK9 gene are associated with hypocholesterolemia and possibly increased response to statin therapy.

OBJECTIVE: The proprotein convertase subtilisin/kexin type 9 (PCSK9) gene encodes a proprotein convertase that causes degradation of cell surface low-density lipoprotein receptors (LDLRs). Mutations in the PCSK9 gene that disrupt the normal function of PCSK9 could therefore result in increased number of LDLRs and hypocholesterolemia. Also, the cholesterol-lowering effect of statins could be increased in subjects carrying mutations in the PCSK9 gene. METHODS AND RESULTS: We have screened 38 unrelated hypocholesterolemic subjects as well as 25 unrelated familial hypercholesterolemia (FH) heterozygotes who responded particularly well to statin therapy for mutations in the 12 exons of the PCSK9 gene by DNA sequencing. Six of the 38 (15.8%) hypocholesterolemic subjects were heterozygous for 1 of the 3 mutations R46L, G106R, or R237W in the PCSK9 gene. In the group of 25 FH heterozygotes who responded particularly well to statin therapy, 3 (8.8%) were heterozygous for mutations R46L or N157K in the PCSK9 gene. None of 441 hypercholesterolemic subjects without mutations in the LDLR gene or in the apolipoprotein B-100 gene possessed any of the 4 mutations. CONCLUSIONS: The 4 missense mutations R46L, G106R, N157K, and R237W are associated with hypocholesterolemia and possibly increased response to statin therapy.

Adult↗
PubMed2006

Novel truncating and missense mutations of the KCC3 gene associated with Andermann syndrome.

BACKGROUND: Andermann syndrome (OMIM 218000) is an autosomal recessive motor-sensory neuropathy associated with developmental and neurodegenerative defects. The cerebral MRI reveals a variable degree of agenesis of the corpus callosum. Recently, truncating mutations of the KCC3 gene (also known as SLC12A6) have been associated with Andermann syndrome. METHODS: The authors assessed clinically and genetically three isolated cases from Germany and Turkey with symptoms consistent with Andermann syndrome. RESULTS: The authors detected four novel mutations within the KCC3 gene in their patients: two different truncating mutations in the first patient, a homozygous truncating mutation in the second, and a homozygous missense mutation in the third patient. In contrast to the classic phenotype of the Andermann syndrome linked to truncating KCC3 mutations the phenotype and the course of the disease linked to the missense mutation appeared to be different (i.e., showing additional features like diffuse and widespread white matter abnormalities). CONCLUSIONS: Not only truncating but also missense mutations of the KCC3 gene are associated with Andermann syndrome. Different types of KCC3 mutations may determine different clinical phenotypes.

Agenesis of Corpus Callosum↗
PubMed2001

Missense mutations of human homeoboxes: A review.

The homeodomain (encoded by the homeobox) is the DNA-binding domain of a large variety of transcriptional regulators involved in controlling cell fate decisions and development. Mutations of homeobox-containing genes cause several diseases in humans. A variety of missense mutations giving rise to human diseases have been described. These mutations are an excellent model to better understand homeodomain molecular functions. To this end, homeobox missense mutations giving rise to human diseases are reviewed. Seventy-four independent homeobox mutations have been observed in 17 different genes. In the same genes, 30 missense mutations outside the homeobox have been observed, indicating that the homeodomain is more easily affected by single amino acids changes than the rest of the protein. Most missense mutations have dominant effects. Several data indicate that dominance is mostly due to haploinsufficiency. Among proteins having the homeodomain as the only DNA-binding domain, three "hot spot" regions can be delineated: 1) at codon encoding for Arg5; 2) at codon encoding for Arg31; and 3) at codons encoding for amino acids of recognition helix. In the latter, mutations at codons encoding for Arg residues at positions 52 and 53 are prevalent. In the recognition helix, Arg residues at positions 52 and 53 establish contacts with phosphates in the DNA backbone. Missense mutations of amino acids that contribute to sequence discrimination (such as those at positions 50 and 54) are present only in a minority of cases. Similar data have been obtained when missense mutations of proteins possessing an additional DNA-binding domain have been analyzed. The only exception is observed in the POU1F1 (PIT1) homeodomain, in which Arg58 is a "hot spot" for mutations, but is not involved in DNA recognition.

Amino Acid Sequence↗
PubMed2000

High metastatic potential in mice inheriting a targeted p53 missense mutation.

To understand the relevance of p53 missense mutations in vivo, we generated a mouse containing an arg-to-his substitution at p53 amino acid 172, which corresponds to the R175H hot-spot mutation in human tumors by homologous recombination. Inadvertently, this mouse contains the additional deletion of a G nucleotide at a splice junction that attenuates levels of mutant p53 to near wild-type levels. Mice heterozygous for the mutant allele differed from p53(+/-) mice in tumor spectrum, with a significant increase in the number of carcinomas and a slight decrease in the number of lymphomas. More importantly, the osteosarcomas and carcinomas that developed in these mutant mice frequently metastasized (69% and 40%, respectively). In contrast, metastasis is rare in osteosarcomas of p53(+/-) mice. Loss of heterozygosity studies of tumors indicated loss of heterozygosity in only 1 of 11 tumors. These data indicate clear differences between a p53 missense mutation and a null allele in tumorigenesis in vivo and suggest that the p53R172HDeltag mutant represents a gain-of-function allele.

Animals↗
PubMed1991

Non-random distribution of missense mutations within the human tyrosinase gene in type I (tyrosinase-related) oculocutaneous albinism.

Type I oculocutaneous albinism (OCA) is produced by mutations of the tyrosinase gene. We report four new missense mutations in the tyrosinase gene in patients with type IA OCA. Three of these mutations occur within exon I and the fourth mutation within exon IV. Analysis of the distribution of these four missense mutations and 12 previously reported missense mutations shows that most cluster in four areas of the gene. Two clusters involve the copper A and copper B binding sites and could disrupt the metal ion-protein interaction necessary for enzyme function. The other two clusters are in exon I and exon IV and could represent important functional domains of the enzyme. We conclude that analysis of the tyrosinase missense mutations will provide insight into the structure-function relationship of this enzyme.

Albinism, Oculocutaneous↗
PubMed2005

Predicting the oncogenicity of missense mutations reported in the International Agency for Cancer Research (IARC) mutation database on p53.

Many mutation databases, comprising thousands of reported mutations, are available. Often the clinical significance of the reported mutations is unknown. In this study we developed an algorithm that allows prediction of the clinical significance of missense mutations reported in a mutation database. Nonsense mutations are used as a referent group for this assessment. We used the International Association for Research on Cancer (IARC) mutation database on TP53 to implement the algorithm. First, on the basis of published data [Nachman MW, Crowell SL. 2000. Genetics 156:297-304], we ascribed mutation rates to every single nucleotide substitution (SNS) in the core domain of the TP53 gene. Second, for every possible SNS we computed the expected number of missense mutations, under the assumption that missense mutations are as oncogenic as nonsense ones. The natural logarithm of the ratio of the observed to the expected number of missense mutations (LR) was used as a quantitative measure of oncogenicity (i.e., the ability of a mutation to produce cancer). We estimated the relative oncogenicity of all missense mutations reported in the IARC p53 mutation database, and constructed a profile of oncogenicity of the missense mutations along the DNA-binding region of p53.

Algorithms↗
PubMed1988

Missense mutation in the lacI gene of Escherichia coli. Inferences on the structure of the repressor protein.

The lac repressor has been studied extensively but a precise three-dimensional structure remains unknown. Studies using mutational data can complement other information and provide insight into protein structure. We have been using the lacI gene-repressor protein system to study the mutational specificity of spontaneous and induced mutation. The sequencing of over 6000 lacI- mutations has revealed 193 missense mutations generating 189 amino acid replacements at 102 different sites within the lac repressor. Replacement sites are not distributed evenly throughout the protein, but are clustered in defined regions. Almost 40% of all sites and over one-half of all substitutions found occur within the amino-terminal 59 amino acid residues, which constitute the DNA-binding domain. The core domain (residues 60 to 360) is less sensitive to amino acid replacement. Here, substitution is found in regions involved in subunit aggregation and at sites surrounding residues that are implicated in sugar-binding. The distribution and nature of missense mutational sites directs attention to particular amino acid residues and residue stretches.

Amino Acid Sequence↗
PubMed2004

Missense mutations in the BRCT domain of BRCA-1 from high-risk women frequently perturb strongly hydrophobic amino acids conserved among mammals.

Inherited missense mutations in the tumor suppressor gene, BRCA-1, may predispose to breast or ovarian cancer, but the exact effects on the protein are generally unknown. The COOH-terminal region of BRCA-1 encodes two BRCT repeats, which are partially conserved in mammalian species (human, dog, rat, and mouse; 60% amino acid identity). A bioinformatic analysis was conducted to evaluate 246 BRCT missense mutations from high-risk breast and/or ovarian cancer patients (reported in the NIH Breast Cancer Information Core database). It was hypothesized that amino acids conserved in evolution would be disproportionately targeted by the mutations and that conserved amino acids with strongly hydrophobic side chains would be disproportionately perturbed. A statistical model was developed, and chi(2) tests were used to determine whether missense mutations are randomly distributed throughout the BRCT repeats or whether they disproportionately target certain amino acids. The results showed that missense mutations disproportionately target amino acids that are identical in all four mammals (chi(2) = 46.01, P < 0.001). In addition, missense mutations disproportionately perturb conserved amino acids with strongly hydrophobic side chains (chi(2) = 68.57, P < 0.001) and alter the strongly hydrophobic property. The two most frequently observed known cancer-predisposing missense mutations in the BRCT repeats, M1775R and A1708E, conform to this pattern. These results suggest that missense mutations affecting highly conserved amino acids with strongly hydrophobic side chains can disturb important features of the BRCA-1 protein and may play a role in breast and ovarian cancer formation.

Amino Acid Sequence↗
PubMed1991

Missense mutations and evolutionary conservation of amino acids: evidence that many of the amino acids in factor IX function as "spacer" elements.

We report 31 point mutations in the factor IX gene and explore the relationship between the level of evolutionary conservation of an amino acid and the probability of a mutation causing hemophilia B. From our total sample of 125 hemophiliacs and from those reported by others, we identify 95 independent missense mutations, 94 of which occur at amino acids that are evolutionarily conserved in the available mammalian factor IX sequences. The likelihood of a missense mutation causing hemophilia B depends on whether the residue is also conserved in the factor IX-related proteases: factor VII, factor X, and protein C. Most of the possible missense mutations in generically conserved residues (i.e., those conserved in factor IX and in all the related proteases) should cause disease. In contrast, missense mutations in factor IX-specific residues (i.e., those conserved in human, cow, dog, and mouse factor IX but not in the related proteases) are sixfold less likely to cause disease. Missense mutations at nonconserved residues are 33-fold less likely to cause disease. At least three models are compatible with these observations. A comparison of sequence alignments from four and nine species of factor IX and an examination of the missense mutations occurring at CpG residues suggest a model in which most residues fall on opposite ends of a spectrum. In about 40% of residues, virtually any missense mutation in a minority of the residues will cause disease, while virtually no missense mutations will cause disease in most of the remaining residues. Thus, many of the residues in factor IX are spacers; that is, the main chains are presumably necessary to keep other amino acid interactions in register, but the nature of the side chain is unimportant.

Amino Acid Sequence↗
PubMed1999

A novel missense mutation (G209R) in exon 8 of the presenilin 1 gene in a Japanese family with presenile familial Alzheimer's disease. Mutation in brief no. 254. Online.

Over fifty missense mutations in the presenilin-1 (PSEN1) gene have been reported in families with presenile familial Alzheimer's disease (FAD). We describe a novel missense mutation (G209R) within the predicted fourth transmembrane domain of the PSEN1 in a Japanese family with presenile FAD. The affected cases showed similar disease histories with the mean age at onset of 49.6 +/- 3.1 years and rapid progressive dementia characterized by memory impairment, amnestic aphasia, disorientation and personality change, but lacking parietal focal symptoms such as apraxia or agnosia. Compared with the previously reported cases of same Gly209 mutation (G209V), the clinical features of the G209R-FAD cases appear to be less critical than those of G209V-FAD cases, although the Gly to Arg mutation is considered to be less conservative than the Gly to Val mutation. These findings may suggest the possible existence of other genetic and/or environmental factors or the possibility that these two different Gly209 mutations may underlie different pathomechanisms in the development of presenile FAD.

Alzheimer Disease↗
PubMed1999

Prognostic significance of p53 mutation in breast cancer: frequent detection of non-missense mutations by yeast functional assay.

p53 status was tested in 180 patients with primary breast cancer using a yeast functional assay. Mutations were identified in 32% of cases. Only half were point missense mutations; the remainder were nonsense, insertion, deletion and splice site mutations. Twenty-two percent of mutations were located outside exons 5-8. For a median follow-up of 88 months, survival analysis showed that p53 mutation conferred a worse prognosis in the whole population and the node-positive subgroup but not in node-negative patients. p53 status, tumour size >2 cm, axillary lymph node metastasis and high histological grade were major adverse risk factors in univariate analysis. Multivariate analysis of 153 patients for whom full data were available showed that p53 status contributed prognostic information when tumour size and lymph node status were taken into account but not when histological grade was included. p53 status thus contributes only limited new prognostic information in breast cancer when established prognostic factors are taken into account. Int. J. Cancer (Pred. Oncol.) 84:587-593, 1999.

Adult↗
PubMed1999

ATP2A2 mutations in Darier's disease: variant cutaneous phenotypes are associated with missense mutations, but neuropsychiatric features are independent of mutation class.

Darier's disease (DD) is an autosomal dominant skin disorder characterized clinically by multiple keratotic papules, and histologically by focal loss of adhesion between epidermal cells (acantholysis) and by abnormal keratinization. Variant forms of cutaneous phenotype, sometimes familial, have been described. Associated neuropsychiatric features, including mental handicap, schizophrenia, bipolar disorder and epilepsy, have also been reported. The cause of DD was shown recently to be mutation in the ATP2A2 gene at 12q24.1, which encodes the sarco-endoplasmic reticulum calcium ATPase type 2 (SERCA2). Here, we show that while both common isoforms of SERCA2 are expressed in the cytoplasm of cultured keratinocytes and fibroblasts, in adult skin sections only the longer isoform, SERCA2b, was expressed abundantly in epidermal structures. Extended mutation analysis in European DD patients using single-strand conformation polymorphism and/or direct sequencing identified 40 different patient-specific mutations in 47 families. The majority (23/40) were likely to result in nonsense-mediated RNA decay. The remaining 17 were missense mutations distributed throughout the protein and were associated significantly with atypical clinical features. The clearest association was with the familial haemorrhagic variant where all four families tested had a missense mutation. Three of the families (one Scottish family and two unrelated Italian families) exhibited the same N767S substitution in the M5 transmembrane domain, and a fourth family, from Sweden, had a C268F substitution in the M3 transmembrane domain. Neuropsychiatric features did not appear to be associated with a specific class of mutation and may be an intrinsic, but inconsistent, effect of defective ATP2A2 expression.

Calcium-Transporting ATPases↗
PubMed1999

Subcortical band heterotopia in rare affected males can be caused by missense mutations in DCX (XLIS) or LIS1.

Subcortical band heterotopia (SBH) are bilateral and symmetric ribbons of gray matter found in the central white matter between the cortex and the ventricular surface, which comprises the less severe end of the lissencephaly (agyria-pachygyria-band) spectrum of malformations. Mutations in DCX (also known as XLIS ) have previously been described in females with SBH. We have now identified mutations in either the DCX or LIS1 gene in three of 11 boys studied, demonstrating for the first time that mutations of either DCX or LIS1 can cause SBH or mixed pachygyria-SBH (PCH-SBH) in males. All three changes detected are missense mutations, predicted to be of germline origin. They include a missense mutation in exon 4 of DCX in a boy with PCH-SBH (R78H), a different missense mutation in exon 4 of DCX in a boy with mild SBH and in his mildly affected mother (R89G) and a missense mutation in exon 6 of LIS1 in a boy with SBH (S169P). The missense mutations probably account for the less severe brain malformations, although other patients with missense mutations in the same exons have had diffuse lissencephaly. Therefore, it appears likely that the effect of the specific amino acid change on the protein determines the severity of the phenotype, with some mutations enabling residual protein function and allowing normal migration in a larger proportion of neurons. However, we expect that somatic mosaic mutations of both LIS1 and DCX will also prove to be an important mechanism in causing SBH in males.

1-Alkyl-2-acetylglycerophosphocholine Esterase↗
PubMed2004

Missense mutations of MADH4: characterization of the mutational hot spot and functional consequences in human tumors.

PURPOSE AND EXPERIMENTAL DESIGN: The mutational spectrum of MADH4 (DPC4/SMAD4) opens valuable insights into the functions of this protein that confer its tumor-suppressive nature in human tumors. We present the MADH4 genetic status determined on a new set of pancreatic, biliary, and duodenal cancers with comparison to the mutational data reported for various tumor types. RESULTS: Homozygous deletion, followed by inactivating nonsense or frameshift mutations, is the predominant form of MADH4 inactivation in pancreatic cancers. Among the naturally occurring MADH4 missense mutations, the MH2 domain is the most frequent target (77%) of missense mutations in human tumors. A mutational hot spot resides within the MH2 domain corresponding to codons 330 to 370, termed the mutation cluster region (MCR). A relationship was found between the locations of the missense mutations (the MH1 domain, the MH2-MCR, and the MH2 outside of the MCR) and the tumor types, suggesting environmental or selective influences in the development of MADH4 mutations. Immunohistochemical studies for Madh4 protein in nine archival cancers (six pancreatic cancers, two duodenal cancers, and one biliary cancer) with known missense mutations indicated that all mutations within the MH1 or MH2 domain COOH-terminal to the MCR (seven of nine cases) had negative or weak labeling, whereas two cancers with mutations within the MCR had strong positive nuclear labeling for Madh4 protein. CONCLUSIONS: These findings have important implications for in vitro functional studies, suggesting that the majority of missense mutations inactivate Madh4 by protein degradation in contrast to those that occur within the MCR.

Animals↗
PubMed2006

PAX6 missense mutations associated in patients with optic nerve malformation.

PURPOSE: PAX6 missense mutations are likely to cause a spectrum of ocular, neurological, and systemic developmental defects and have been reported in various ethnic groups. The purpose of this study was to investigate the clinical features of optic nerve malformation caused by PAX6 mutations in Indian patients. METHODS: Total genomic DNA was isolated from peripheral blood of 27 sporadic probands affected with congenital optic nerve malformation, unaffected family members, and 50 unrelated age-matched controls. Informed consent was obtained from all study subjects. Polymerase chain reaction was carried out to explore PAX6 defective alleles using single-strand conformation analysis (PCR-SSCA) followed by automated bidirectional sequencing. RESULTS: We identified two novel PAX6 missense mutations in two unrelated sporadic probands. The mutation analysis revealed variation at position c.469G>C, codon 36 in proband ONH 4-1 with optic nerve hypoplasia. The other de novo mutation was observed at c.514G>C, codon 51 in proband ODC 5-1 with optic disc coloboma. Both G>C base substitutions cause a relatively conservative amino acid change, altering glycine to alanine residues within the paired DNA-binding domain. CONCLUSIONS: In this study, we have been able to identify two sequence variations in the PAX6 gene. These missense mutations may uniquely alter the structure and expression of PAX6 protein, resulting in distinct clinical phenotypes. Mutation analysis of 27 probands for PAX6 has resulted in only two significant variants. This finding demonstrated that the frequency of PAX6 mutations associated with optic nerve malformation is low, requiring the elucidation of other candidate genes in other patients.

Adolescent↗
PubMed2006

Assessing the pathogenicity of MLH1 missense mutations in patients with suspected hereditary nonpolyposis colorectal cancer: correlation with clinical, genetic and functional features.

Assessing the pathogenicity of missense mutations of MLH1 and MSH2 is critical to counsel patients with suspected hereditary nonpolyposis colorectal cancer (HNPCC). Approximately 32% of all MLH1 mutations and 18% of MSH2 mutations are missense variants which often have an uncertain genetic significance. To assess the pathogenicity of four MLH1 missense mutations which were found in five patients with suspected HNPCC, P648S (CCC --> TCC), L559R (CTG --> CGG), K618A (AAG --> GCG), Y646C (TAT --> TGT), we studied their ability to disrupt MLH1 protein function and their relationship with all those clinical, genetic and pathological features which are typical of this syndrome. Our results indicated that the P648S and L559R mutations were probably pathogenic because they disrupted MLH1 protein interaction with its partner PMS2 in vitro and abolished MLH1 expression in HCT116 cells. In addition these variants were associated with features often found in HNPCC patients: in particular high microsatellite instability, occurrence of high grade tumours and, in one case, strong family history. The pathogenicity of the K618A and Y646C mutations was questionable as their correlation with features typical of HNPCC was low and the outcome of the functional analysis was ambiguous. These observations suggested that a clinically usable assessment of the pathogenicity of MLH missense variants can be achieved through the analysis of multiple mutation characteristics among which loss of protein function, occurrence of microsatellite instability and family history seemed to have a predominant role.

Adaptor Proteins, Signal Transducing↗