Nonsense Polymorphism Research Articles

T Allele of nonsense polymorphism (rs2039381, Gln71Stop) of interferon-ε is a risk factor for the development of intracerebral hemorrhage

Interferons (IFNs) play key roles in various biologic responses including antiviral and immune reactions. We evaluated one possible risk factor in nonsense polymorphism (rs2039381, Gln71Stop) of interferon-ε (IFNE).We recruited stroke [119 ischemic stroke (IS) and 145 intracerebral hemorrhage (ICH)] and control (401), respectively. The nonsense SNP (rs2039381, Gln71Stop) of IFNE was selected. We identified individual genotype using sequencing. SNPStats and SPSS 18.0 programs were used to analyze genetic data. Genotype frequencies (C/C:C/T:T/T) in the ICH group and control group were 59.3:37.9:2.8 and 73.6:23.4:3.0, respectively. We found that rs2039381 was associated with ICH (OR=2.01, 95% CI=1.33–3.03, p=0.001 in codominant1 model; OR=1.91, 95% CI=1.28–2.84, p=0.0016 in dominant model; OR=1.60, 95% CI=1.14–2.26, p=0.0074 in log-additive model). T allele frequency of rs2039381 was significantly higher in ICH than in controls. The nonsense SNP (rs2039381, Gln71Stop) of IFNE was associated with ICH (OR=1.61, 95% CI=1.14–2.26, p=0.006).A nonsense SNP (rs2039381, Gln71Stop) of IFNE was associated with ICH in Korean population. Our findings raise the possibility that the T allele of rs2039381 is a risk factor which is susceptible to ICH.

ACTN3 genotype influences muscle performance through the regulation of calcineurin signaling

α-Actinin-3 deficiency occurs in approximately 16% of the global population due to homozygosity for a common nonsense polymorphism in the ACTN3 gene. Loss of α-actinin-3 is associated with reduced power and enhanced endurance capacity in elite athletes and nonathletes due to "slowing" of the metabolic and physiological properties of fast fibers. Here, we have shown that α-actinin-3 deficiency results in increased calcineurin activity in mouse and human skeletal muscle and enhanced adaptive response to endurance training. α-Actinin-2, which is differentially expressed in α-actinin-3-deficient muscle, has higher binding affinity for calsarcin-2, a key inhibitor of calcineurin activation. We have further demonstrated that α-actinin-2 competes with calcineurin for binding to calsarcin-2, resulting in enhanced calcineurin signaling and reprogramming of the metabolic phenotype of fast muscle fibers. Our data provide a mechanistic explanation for the effects of the ACTN3 genotype on skeletal muscle performance in elite athletes and on adaptation to changing physical demands in the general population. In addition, we have demonstrated that the sarcomeric α-actinins play a role in the regulation of calcineurin signaling.

Association study between nonsense polymorphism (rs2039381, Gln71Stop) of Interferon-ε and susceptibility to vitiligo in Korean population

Interferons (IFNs) are related to autoimmune responses. IFN-epsilon (IFNE) is included in IFN family, and may modulate immunological functions. Inflammation modulating functions of IFNE may be related with the pathophysiology of vitiligo. To investigate the association of nonsense polymorphism (rs2039381, Gln71Stop) of interferon-ε (IFNE) and susceptibility to vitiligo, we conducted a case-control association study in 265 non-segmental vitiligo (NSV) patients and 320 healthy controls. The nonsense single nucleotide polymorphism (SNP) (rs2039381, Gln71Stop) of IFNE was genotyped by direct sequencing. Multiple logistic regression models (log-additive, dominant, and recessive models) were applied to determine odds ratios (OR), 95% confidence interval (CI), and p values. The rs2039381 (Gln71Stop) of IFNE did not show significant differences between NSV patient group and control group. However, we found that in childhood onset NSV groups, the IFNE nonsense polymorphism (rs2039381, Gln71Stop) showed a significant association. There was significantly different distribution of nonsense polymorphism of rs2039381 (Gln71Stop) of IFNE between NSV patients (childhood <18 years) and control subjects. This study suggests that rs2039381 (Gln71Stop) polymorphism of IFNE may be related to onset time of vitiligo in NSV patients.

A Nonsense Polymorphism (R392X) in TLR5 Protects from Obesity but Predisposes to Diabetes

The TLR5 gene encodes an innate immunity receptor. Mice lacking Tlr5 (T5KO) develop insulin resistance and increased adiposity. Owing to the segregation of a dominant nonsense polymorphism (R392X, rs5744168), a portion of humans lack TLR5 function. We investigated whether the nonsense polymorphism influences obesity and susceptibility to type 2 diabetes (T2D). R392X was genotyped in two cohorts from Saudi Arabia, a region where obesity and type 2 diabetes (T2D) are highly prevalent. The nonsense allele was found to protect from obesity (p(combined) = 0.0062; odds ratio, 0.51) and to associate with lower body mass index (BMI) (p(combined) = 0.0061); this allele also correlated with a reduced production of proinflammatory cytokines. A significant interaction was noted between rs5744168 and sex in affecting BMI (p(interaction) = 0.006), and stratification by gender revealed that the association is driven by females (p(combined) = 0.0016 and 0.0006 for obesity and BMI, respectively). The nonsense polymorphism also associated with BMI in nonobese women. After correction for BMI, the 392X allele was found to represent a risk factor for T2D with a sex-specific effect (p(interaction) = 0.023) mediated by females (p = 0.021; odds ratio, 2.60). Fasting plasma glucose levels in nondiabetic individuals were also higher in women carrying the nonsense allele (p = 0.012). Thus, in contrast to T5KO mice, loss of human TLR5 function protects from weight gain, but in analogy to the animal model, the nonsense allele predisposes to T2D. These effects are apparently sex-specific. Data in this study reinforce the hypothesis that metabolic diseases, including T2D, are associated with immune dysregulation.

Genome-wide survey of interindividual differences of RNA stability in human lymphoblastoid cell lines

The extent to which RNA stability differs between individuals and its contribution to the interindividual expression variation remain unknown. We conducted a genome-wide analysis of RNA stability in seven human HapMap lymphoblastoid cell lines (LCLs) and analyzed the effect of DNA sequence variation on RNA half-life differences. Twenty-six percent of the expressed genes exhibited RNA half-life differences between LCLs at a false discovery rate (FDR) < 0.05, which accounted for ~ 37% of the gene expression differences between individuals. Nonsense polymorphisms were associated with reduced RNA half-lives. In genes presenting interindividual RNA half-life differences, higher coding GC3 contents (G and C percentages at the third-codon positions) were correlated with increased RNA half-life. Consistently, G and C alleles of single nucleotide polymorphisms (SNPs) in protein coding sequences were associated with enhanced RNA stability. These results suggest widespread interindividual differences in RNA stability related to DNA sequence and composition variation.

A case report of a novel homozygote mutation causing severe Leydig cell hypoplasia: insights in the coexistence of nonsense mutation and polymorphism in the same LHCGR gene locus

Introduction: Leydig cell hypoplasia is a rare autosomal recessive condition that interferes with normal development of male external genitalia in 46,XY individuals. It is mediated by mutations in the lutropin/choriogonadotropin receptor (LHCGR) gene, resulting in impairment of either hormone binding or signal transduction. Case report: We report a 32-year-old female patient who presented with primary amenorrhoea, female external genitalia and 46,XY karyotype. Breast and pubic hair development were of B2 and PH2 respectively. Magnetic resonance imaging revealed at both sides inguinal testicles (cryptorchidism) with microcalcification in the absence of uterus and ovaries. At first presentation, serum luteinizing hormone was about 3-fold above the normal limit, while testosterone was in the normal female adult range. Estradiol was low and the serum follicle-stimulating hormone was unremarkable. Dehydroepiandrosterone sulphate, 17-hydroxyprogesterone and sex hormone-binding globulin were normal. Anti-Mullerian hormone and inhibin B were elevated. Mutation or deletion of the sex-determining region Y-, androgen receptor- and steroid 5-alpha-reductase-gene could be excluded. Finally, sequencing of the lutropin-choriogonadotropic hormone receptor gene revealed a homozygote nonsense mutation in exon 10 (c.907C>T, p.Gln 303Trm). Interestingly, a second a second polymorphism was found (c.935A>G, p.Asn312Ser) downstream of the disruption of the gene sequence. We therefore concluded to the diagnosis of severe Leydig cell hypoplasia. A hormone replacement therapy with estradiol was inducted and the further operative removal of the inguinal testicles as well as the genetic analysis of the parents is planned. Conclusions: We report a phenotypically female patient with 46,XY disorder of sexual development with a novel homozygote nonsense mutation (p.Gln303Trm) accompanied by a second homozygote polymorphism (p.Asn312Ser) in the LHCGR gene. Our case expands the genotypic spectrum of LHCGR mutations and underlines the importance of thorough molecular analysis.

Role of alpha-actinin-3 in contractile properties of human single muscle fibers: a case series study in paraplegics.

A common nonsense polymorphism in the ACTN3 gene results in the absence of α-actinin-3 in XX individuals. The wild type allele has been associated with power athlete status and an increased force output in numeral studies, though the mechanisms by which these effects occur are unclear. Recent findings in the Actn3−/− (KO) mouse suggest a shift towards ‘slow’ metabolic and contractile characteristics of fast muscle fibers lacking α-actinin-3. Skinned single fibers from the quadriceps muscle of three men with spinal cord injury (SCI) were tested regarding peak force, unloaded shortening velocity, force-velocity relationship, passive tension and calcium sensitivity. The SCI condition induces an ‘equal environment condition’ what makes these subjects ideal to study the role of α-actinin-3 on fiber type expression and single muscle fiber contractile properties. Genotyping for ACTN3 revealed that the three subjects were XX, RX and RR carriers, respectively. The XX carrier’s biopsy was the only one that presented type I fibers with a complete lack of type IIx fibers. Properties of hybrid type IIa/IIx fibers were compared between the three subjects. Absence of α-actinin-3 resulted in less stiff type IIa/IIx fibers. The heterozygote (RX) exhibited the highest fiber diameter (0.121±0.005 mm) and CSA (0.012±0.001 mm2) and, as a consequence, the highest peak force (2.11±0.14 mN). Normalized peak force was similar in all three subjects (P = 0.75). Unloaded shortening velocity was highest in R-allele carriers (P<0.001). No difference was found in calcium sensitivity. The preservation of type I fibers and the absence of type IIx fibers in the XX individual indicate a restricted transformation of the muscle fiber composition to type II fibers in response to long-term muscle disuse. Lack of α-actinin-3 may decrease unloaded shortening velocity and increase fiber elasticity.

The JR blood group system (ISBT 032): molecular characterization of three new null alleles

Jr(a) (ISBT 901005) is a high-prevalence antigen unassigned to a blood group system. People lacking this antigen have been found in all populations studied but most commonly in Asians. Two recent reports established that ABCG2-null alleles encode the Jr(a-) phenotype and these studies provided the impetus to study other Jr(a-) individuals. Blood samples were part of our rare donor-patient collection. DNA was isolated and analyzed by standard techniques. In samples from 13 Jr(a-) study subjects, we found six alleles with nonsense nucleotide changes, three (c.784T, c.1591T, and c.337T) were novel. Twelve of the samples were homozygous for nonsense single-nucleotide polymorphisms (SNPs): eight were c.376T, two were c.706T, one was c.784T, and one was c.1591T. Each of these alleles predicts a truncated ABCG2 product, Gln126Stop, Arg236Stop, Gly262Stop, and Gln531Stop, respectively. One study subject was heterozygous for two nonsense SNPs: c.337C/T (Arg113Stop) and c.736C/T (Arg246Stop). Jr(a) is the sole antigen in the newly established JR blood group system (ISBT 032001). The previous ISBT designation (901005) is now obsolete. Since ABCG2null alleles define the Jr(a-) phenotype, an explanation for why no antithetical low-prevalence antigen to Jr(a) has been found, and also why anti-Jr(a) made by people with any of these JRnull alleles are mutually compatible has been determined. Based on our findings DNA-based genotyping can be developed to replace the serologic methods that are currently used to identify Jr(a-) blood donors.

Genome-Wide Association Studies Identify Heavy Metal ATPase3 as the Primary Determinant of Natural Variation in Leaf Cadmium in Arabidopsis thaliana

Understanding the mechanism of cadmium (Cd) accumulation in plants is important to help reduce its potential toxicity to both plants and humans through dietary and environmental exposure. Here, we report on a study to uncover the genetic basis underlying natural variation in Cd accumulation in a world-wide collection of 349 wild collected Arabidopsis thaliana accessions. We identified a 4-fold variation (0.5–2 µg Cd g−1 dry weight) in leaf Cd accumulation when these accessions were grown in a controlled common garden. By combining genome-wide association mapping, linkage mapping in an experimental F2 population, and transgenic complementation, we reveal that HMA3 is the sole major locus responsible for the variation in leaf Cd accumulation we observe in this diverse population of A. thaliana accessions. Analysis of the predicted amino acid sequence of HMA3 from 149 A. thaliana accessions reveals the existence of 10 major natural protein haplotypes. Association of these haplotypes with leaf Cd accumulation and genetics complementation experiments indicate that 5 of these haplotypes are active and 5 are inactive, and that elevated leaf Cd accumulation is associated with the reduced function of HMA3 caused by a nonsense mutation and polymorphisms that change two specific amino acids.

Sodium Current and Potassium Transient Outward Current Genes in Brugada Syndrome: Screening and Bioinformatics

BackgroundBrugada syndrome (BrS) is a primary arrhythmia syndrome characterized by the occurrence of malignant ventricular arrhythmias. Previously, the genes SCN1B, SCN3B, MOG1, and KCND3 have been associated with BrS. Recent data from exome screening efforts permit better discrimination between low-frequency genetic variants and true monogenetic disease-causing variants. We aimed to screen the genes SCN1B through SCN4B, MOG1, CAV3, and KCND3 for variations in a population of SCN5A negative Danish and Iranian BrS patients, as well as research prior associations using newly released exome data. MethodsScreening of all exons and splice sites was performed using Sanger sequencing. Bioinformatic searches were performed in the Single-nucleotide polymorphism database (build 132) and in the National Heart, Lung, and Blood Institute Grand Opportunity Exome Sequencing Project (ESP) for both previously published variant-BrS associations and newly uncovered variations within the noted genes. ResultsA total of 42 BrS patients were screened, and 2 different nonsynonymous mutations in SCN1Bb (H162P and R214Q) were found in 2 different Danish patients. The variants were not found in 216 Danish controls, but R214Q was present in ESP data (5 of 841 alleles). No other mutations were found. Previously BrS-associated mutations in KNCD3 and SCN3B were also present in ESP data. This was not the case for MOG1, but a nonsense polymorphism was present in 0.5% of alleles. ConclusionsOur study supports the association of SCN1Bb with BrS. However, recently released exome data make some of the prior associations of BrS with genes SCN3B, MOG1, and KCND3 less likely.

Association of the R67X and W303X non-sense polymorphisms in the protein Z-dependent protease inhibitor gene with idiopathic recurrent miscarriage

Protein Z-dependent protease inhibitor (ZPI) is a 72 kDa single-chain serpin which inhibits the activated coagulation factors X and XI. Two non-sense polymorphisms of ZPI, R67X and W303X, were recently identified, and were linked with a prothrombotic state. Here, we investigated the association of the R67X (728C>T) and W303X (1438G>A) variants in the ZPI gene with recurrent spontaneous miscarriage (RSM). This was a case-control study involving a total of 288 women with a history of two consecutive or ≥3 non-consecutive pregnancy losses between 8 and 12th week of gestation, along with 304 age-matched and ethnically matched multiparous control women, with no personal or family history of pregnancy complications. The minor allele frequency of R67X (P = 0.003) and W303X (P = 0.014) were higher in RSM cases than in control women. Both single-nucleotide polymorphisms were significantly associated with RSM under the dominant genetic association model, and were in moderate linkage disequilibrium (D' = 0.412; P < 0.001). Taking the common (728)C/(1438)G haplotype as reference, multivariate analysis confirmed the positive association of (728)T/(1438)G [P = 0.043; odds ratio (OR) = 2.25; 95% confidence interval (CI) = 1.03-4.90], and (728)T/(1438)A (P = 0.022; OR = 3.93; 95% CI = 1.23-12.59) haplotypes with increased RSM risk. These differences remained significant after controlling for some covariates. These results demonstrate that both ZPI R67X and W303X non-sense variants and specific ZPI haplotypes are significantly associated with RSM.

Association of the ACTN3 R577X Polymorphism in Polish Power-Orientated Athletes

Alpha-actinins are an ancient family of actin-binding proteins that play structural and regulatory roles in cytoskeletal organization. In skeletal muscle, α-actinin-3 protein is an important structural component of the Z disc, where it anchors actin thin filaments, helping to maintain the myofibrillar array. A common nonsense polymorphism in codon 577 of the ACTN3 gene (R577X) results in α-actinin-3 deficiency in XX homozygotes. Based on knowledge about the role of ACTN3 R557X polymorphism in skeletal muscle function, we postulated that the genetic polymorphism of ACTN3 could also improve sprint and power ability.We compared genotypic and allelic frequencies of the ACTN3 R557X polymorphism in two groups of men of the same Caucasian descent: 158 power-orientated athletes and 254 volunteers not involved in competitive sport.The genotype distribution in the group of power-oriented athletes showed significant differences (P=0.008) compared to controls. However, among the investigated subgroups of athletes, only the difference of ACTN3 R577X genotype between sprinters and controls reached statistical significance (P=0.041). The frequencies of the ACTN3 577X allele (30.69% vs. 40.35%; P=0.005) were significantly different in all athletes compared to controls.Our results support the hypothesis that the ACTN3 577XX allele may have some beneficial effect on sprint-power performance, because the ACTN3 XX genotype is significantly reduced in Polish power-oriented athletes compared to controls. This finding seems to be in agreement with previously reported case-control studies. However, ACTN3 polymorphism as a genetic marker for sport talent identification should be interpreted with great caution.

Advances in Exercise, Fitness, and Performance Genomics in 2010

This review of the exercise genomics literature emphasizes the strongest articles published in 2010 as defined by sample size, quality of phenotype measurements, quality of the exercise program or physical activity exposure, study design, adjustment for multiple testing, quality of genotyping, and other related study characteristics. One study on voluntary running wheel behavior was performed in 448 mice from 41 inbred strains. Several quantitative trait loci for running distance, speed, and duration were identified. Several studies on the alpha-3 actinin (ACTN3) R577X nonsense polymorphism and the angiotensin-converting enzyme (ACE) I/D polymorphism were reported with no clear evidence for a joint effect, but the studies were generally underpowered. Skeletal muscle RNA abundance at baseline for 29 transcripts and 11 single nucleotide polymorphisms (SNPs) were both found to be predictive of the V˙O2max response to exercise training in one report from multiple laboratories. None of the 50 loci associated with adiposity traits are known to influence physical activity behavior. However, physical activity seems to reduce the obesity-promoting effects of at least 12 of these loci. Evidence continues to be strong for a role of gene-exercise interaction effects on the improvement in insulin sensitivity after exposure to regular exercise. SNPs in the cAMP-responsive element binding position 1 (CREB1) gene were associated with training-induced HR response, in the C-reactive protein (CRP) gene with training-induced changes in left ventricular mass, and in the methylenetetrahydrofolate reductase (MTHFR) gene with carotid stiffness in low-fit individuals. We conclude that progress is being made but that high-quality research designs and replication studies with large sample sizes are urgently needed.

A Novel Pathogenic Nonsense Triple-Nucleotide Mutation in the Low-Density Lipoprotein Receptor Gene and Its Clinical Correlation with Familial Hypercholesterolemia

The aim of this study was to determine the genetic basis of familial hypercholesterolemia in a Pakistani family with a history of myocardial infarction and premature coronary artery disease. Direct sequencing of the low-density lipoprotein receptor gene resulted in the identification of a novel missense mutation c.264G>C (p.R88S) in exon 3 and a novel nonsense triple-nucleotide polymorphism (TNP) c.887-889GCA>AGC (p.C296X) in exon 6, the latter being probably the disease-causing mutation in this family. Both of these mutations were not present in the probands of 14 familial hypercholesterolemia families, 100 myocardial infarction patients, as well as 150 normolipidemic ethnically matched control individuals. The identification of the novel nonsense TNP is the first report of a nonsense pathogenic TNP in low-density lipoprotein receptor or any other gene and only the fourth report of a pathogenic TNP of any type, which emphasizes the importance of screening for TNPs in patients and in familial studies that might otherwise be missed if only analyzed on single-nucleotide polymorphism arrays.

The effect of α-actinin-3 deficiency on muscle aging

Deficiency of the fast-twitch muscle protein α-actinin-3 due to homozygosity for a nonsense polymorphism (R577X) in the ACTN3 gene is common in humans. α-Actinin-3 deficiency (XX) is associated with reduced muscle strength/power and enhanced endurance performance in elite athletes and in the general population. The association between R577X and loss in muscle mass and function (sarcopenia) has previously been investigated in a number of studies in elderly humans. The majority of studies report loss of ACTN3 genotype association with muscle traits in the elderly, however, there is some indication that the XX genotype may be associated with faster muscle function decline. To further explore these potential age-related effects and the underlying mechanisms, we examined the effect of α-actinin-3 deficiency in aging male and female Actn3 knockout (KO) mice (2, 6, 12, and 18months). Our findings support previous reports of a diminished influence of ACTN3 genotype on muscle performance in the elderly: genotype differences in intrinsic exercise performance, fast muscle force generation and male muscle mass were lost in aged mice, but were maintained for other muscle function traits such as grip strength. The loss of genotype difference in exercise performance occurred despite the maintenance of some “slower” muscle characteristics in KO muscles, such as increased oxidative metabolism and greater force recovery after fatigue. Interestingly, muscle mass decline in aged 18month old male KO mice was greater compared to wild-type controls (WT) (−12.2% in KO; −6.5% in WT). These results provide further support that α-actinin-3 deficient individuals may experience faster decline in muscle function with increasing age.

Chemotherapeutic drug susceptibility associated SNPs are enriched in expression quantitative trait loci

Pharmacogenomics has employed candidate gene studies and, more recently, genome-wide association studies (GWAS) in efforts to identify loci associated with drug response and/or toxicity. The advantage of GWAS is the simultaneous, unbiased testing of millions of SNPs; the challenge is that functional information is absent for the vast majority of loci that are implicated. In the present study, we systematically evaluated SNPs associated with chemotherapeutic agent-induced cytotoxicity for six different anticancer agents and evaluated whether these SNPs were disproportionately likely to be within a functional class such as coding (consisting of missense, nonsense, or frameshift polymorphisms), noncoding (such as 3'UTRs or splice sites), or expression quantitative trait loci (eQTLs; indicating that a SNP genotype is associated with the transcript abundance level of a gene). We found that the chemotherapeutic drug susceptibility-associated SNPs are more likely to be eQTLs, and, in fact, more likely to be associated with the transcriptional expression level of multiple genes (n > or = 10) as potential master regulators, than a random set of SNPs in the genome, conditional on minor allele frequency. Furthermore, we observed that this enrichment compared with random expectation is not present for other traditionally important coding and noncoding SNP functional categories. This research therefore has significant implications as a general approach for the identification of genetic predictors of drug response and provides important insights into the likely function of SNPs identified in GWAS analysis of pharmacologic studies.

Advances in Exercise, Fitness, and Performance Genomics

An annual review publication of the most significant articles in exercise, fitness, and performance genomics begins with this article, which covers 2 yr, 2008 and 2009. The review emphasizes the strongest articles as defined by sample size, quality of phenotype measurements, quality of the exercise program or physical activity exposure, study design, adjustment for multiple testing, quality of genotyping, and other related study characteristics. With this avowed focus on the highest quality articles, only a small number of published articles are reviewed. Among the most significant findings reported here are a brief overview of the first genome-wide association study of the genetic differences between exercisers and nonexercisers. In addition, the latest results on the actinin alpha 3 (ACTN3) R577X nonsense polymorphism are reviewed, emphasizing that no definitive conclusion can be reached at this time. Recent studies that have dealt with mitochondrial DNA haplogroups and endurance performance are described. Published reports indicating that physical activity may attenuate the effect of the fat mass and obesity associated (FTO) gene risk allele on body mass index are reviewed. Articles that have tested the contributions of specific genes to the response of glucose and insulin metabolism traits to regular exercise or physical activity level are considered and found to be generally inconclusive at this stage. Studies examining ethnic differences in the response of blood lipids and lipoproteins to exercise training cannot unequivocally relate these to apolipoprotein E (APOE) genotypes. Hemodynamic changes with exercise training were reported to be associated to sequence variation in kinesin heavy chain (KIF5B), but no replication study is available as of yet. We conclude from this first installment that exercise scientists need to prioritize high-quality research designs and that replication studies with large sample sizes are urgently needed.

Distribution and Effects of Nonsense Polymorphisms in Human Genes

BackgroundA great amount of data has been accumulated on genetic variations in the human genome, but we still do not know much about how the genetic variations affect gene function. In particular, little is known about the distribution of nonsense polymorphisms in human genes despite their drastic effects on gene products.Methodology/Principal FindingsTo detect polymorphisms affecting gene function, we analyzed all publicly available polymorphisms in a database for single nucleotide polymorphisms (dbSNP build 125) located in the exons of 36,712 known and predicted protein-coding genes that were defined in an annotation project of all human genes and transcripts (H-InvDB ver3.8). We found a total of 252,555 single nucleotide polymorphisms (SNPs) and 8,479 insertion and deletions in the representative transcripts in these genes. The SNPs located in ORFs include 40,484 synonymous and 53,754 nonsynonymous SNPs, and 1,258 SNPs that were predicted to be nonsense SNPs or read-through SNPs. We estimated the density of nonsense SNPs to be 0.85×10−3 per site, which is lower than that of nonsynonymous SNPs (2.1×10−3 per site). On average, nonsense SNPs were located 250 codons upstream of the original termination codon, with the substitution occurring most frequently at the first codon position. Of the nonsense SNPs, 581 were predicted to cause nonsense-mediated decay (NMD) of transcripts that would prevent translation. We found that nonsense SNPs causing NMD were more common in genes involving kinase activity and transport. The remaining 602 nonsense SNPs are predicted to produce truncated polypeptides, with an average truncation of 75 amino acids. In addition, 110 read-through SNPs at termination codons were detected.Conclusion/SignificanceOur comprehensive exploration of nonsense polymorphisms showed that nonsense SNPs exist at a lower density than nonsynonymous SNPs, suggesting that nonsense mutations have more severe effects than amino acid changes. The correspondence of nonsense SNPs to known pathological variants suggests that phenotypic effects of nonsense SNPs have been reported for only a small fraction of nonsense SNPs, and that nonsense SNPs causing NMD are more likely to be involved in phenotypic variations. These nonsense SNPs may include pathological variants that have not yet been reported. These data are available from Transcript View of H-InvDB and VarySysDB (http://h-invitational.jp/varygene/).

Polymorphisms of the Z protein protease inhibitor and risk of venous thromboembolism: a meta‐analysis

Two nonsense polymorphisms of Z-dependent protease inhibitor (ZPI; Serpina10) have been identified. To assess the risk of venous thromboembolism (VTE) associated with W303x and R67X Serpina10 mutations, we performed a meta-analysis of studies comparing the prevalence of these two mutations in VTE patients and in controls Odds Ratios (ORs) and 95% confidence intervals (CIs) were calculated for each trial and pooled using a random-effects model. Five studies involving 5000 patients were included. R67X and W303X mutations of Serpina10 were not associated with increased VTE risk (OR 1.63; 95% CI 0.84, 3.16 and OR 1.21; 95% CI 0.29, 4.98 respectively).

Renin‐Angiotensin System Polymorphisms and Risk of Hypertension: Influence of Environmental Factors

Renin-angiotensin system (RAS) polymorphisms have been studied as candidate risk factors for hypertension with inconsistent results, possibly due to heterogeneity among various environmental factors. We analyzed the association between RAS candidate gene polymorphisms and risk of hypertension among 2722 women and also explored whether these associations varied according to menopausal status, body mass index, and dietary factors. In a main-effects analysis of all 2722 women adjusted for age and race, homozygosity for the AT1R A1166C polymorphism was associated with hypertension (odds ratio, 1.35; 95% confidence interval [CI], 1.03-1.78). We also found that a novel nonsense polymorphism in the aminopeptidase-A gene was associated with hypertension among postmenopausal women (hazard ratio, 1.54; 95% CI, 1.01-2.37), women with inadequate calcium intake (hazard ratio, 2.47; 95% CI, 1.29-4.72) and, marginally, women with inadequate vitamin D intake. In addition, angiotensin-converting enzyme and AT1R A1166C polymorphisms were associated or marginally associated with incident hypertension among postmenopausal women and those with inadequate calcium and vitamin D intakes. These data suggest that demographic and dietary factors may influence the associations between RAS polymorphisms and hypertension and could explain heterogeneity in prior studies.