Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Genetic variant”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 91 records · Page 5Linked to original sources
PubMed1997

Different susceptibilities of genetic variants of hepatitis C virus (HCV) to interferon (IFN).

Genetic variants of HCV may have different degrees of resistance to IFN and may therefore influence the outcome of IFN therapy. However, selection of HCV variants by IFN has not been investigated in detail. In this paper, heteroduplex analysis was used to monitor major changes of HCV populations in 4 chronically infected patients under IFN therapy. We found that a major variant of the HCV 5' non-coding region (5' NCR) emerged in a responder. In other patients although no new variant of the 5' NCR was identified, significant changes occurred within the core and E1 region of the HCV genome. Disappearance and emergence of HCV variants may reflect their different susceptibilities to IFN. Our results indicate that responses of HCV populations to IFN are complex and need to be characterized by analysis of multiple HCV genome regions.

Antiviral Agents↗
PubMed1991

On the origins of genetic variants.

Two contrasting mechanisms responsible for the creation of genetic variants are described: one is the manifestation of the limited accuracy of the cellular machinery for DNA replication, the other results from the ability of cells to repair damaged DNA. Replication-dependent variants and those caused by episodical DNA damage enhance the probability that a small fraction of a cell population may survive a sudden (physical or biological) change of environmental conditions. Replication-independent variants arise during persistent but not immediately lethal stress (e.g. starvation) of a non-dividing population. The variants observed under these conditions are of selective advantage because they are able to cope with the particular stress situation. The molecular basis of their creation is a matter of intensive debate.

Biological Evolution↗
PubMed2006

A common genetic variant in the NOS1 regulator NOS1AP modulates cardiac repolarization.

Extremes of the electrocardiographic QT interval, a measure of cardiac repolarization, are associated with increased cardiovascular mortality. We identified a common genetic variant influencing this quantitative trait through a genome-wide association study on 200 subjects at the extremes of a population-based QT interval distribution of 3,966 subjects from the KORA cohort in Germany, with follow-up screening of selected markers in the remainder of the cohort. We validated statistically significant findings in two independent samples of 2,646 subjects from Germany and 1,805 subjects from the US Framingham Heart Study. This genome-wide study identified NOS1AP (CAPON), a regulator of neuronal nitric oxide synthase, as a new target that modulates cardiac repolarization. Approximately 60% of subjects of European ancestry carry at least one minor allele of the NOS1AP genetic variant, which explains up to 1.5% of QT interval variation.

Adaptor Proteins, Signal Transducing↗
PubMed1997

Red cell acetyl cholinesterase and plasma cholinesterase activity and genetic variants of plasma cholinesterase in northwest Indian adults.

The plasma cholinesterase (PChE) and red cell acetyl cholinesterase (AChE) activities are indicators of exposure to organophosphates. We studied their distribution in unexposed Northwest Indian adults by measuring them in 120 men and 111 women by Ellman's and Kalow's method, respectively. We also determined genetic variability of plasma cholinesterase in 193 subjects (male = 111, female = 82). The mean +/- (SD) AChE levels in population, men and women, were 34.97 +/- 13.66, 35.05 +/- 12.42, 34.88 +/- 14.89 nmol/mg Hb/min, whereas PChE was 0.448 +/- 0.173, 0.435 +/- 0.163, 0.462 +/- 0.183 ku/l, respectively. When compared for sex, no significant difference could be found for red cell AChE and PChE activity. However, on 2-way analysis of variance (ANOVA) adjusted for age classification, the levels of both AChE and PChE were significantly higher in groups above the age of 30 years as compared to below 30 years (t = 3.08, p < 0.01, t = 2.82, p < 0.05), respectively. Seven genetic variants of PChE could be detected in males, whereas in females 6 genetic variants were found.

Acetylcholinesterase↗
PubMed1991

Albumin Paris 2: a new genetic variant distinguished by isoelectric focusing.

Until recently, the characterization of genetic variants of human serum albumin was performed by electrophoretic typing prior to the determination of their amino acid substitutions. We describe a procedure using isoelectric focusing in the presence of urea for the analysis of the genetic variation of albumin. This procedure allowed a clear distinction of a new variant, previously found to be identical with albumin Sondrio according to its relative electrophoretic mobilities at 3 pHs. This new variant, the third rare albumin allotype identified in the Ile-de-France region, was called albumin Paris 2.

Amino Acid Sequence↗
PubMed2004

[Influence of human genetic variants on resistance and immunity against malaria].

Certain human genetic variants occur on-ly in areas endemic for malaria. They protect against fatal malaria complications and cause inhibition of growth or development of malaria parasites in vitro. Among these are the haemoglobins (Hb) S and C, alpha-thalassaemias, glucose-6-phosphate dehydrogenase deficiency, as well as a deletion in the erythrocyte band 3 protein. Evidence for similar effects has been obtained for HbD and HbE, glycophorins A and C as well as for a number of immunologically relevant molecules such as human leukocyte antigens,tumour-necrosis-factor a and the inducible nitric oxide synthase. The findings indicate that malaria in endemic areas has caused a substantial selection of the human genome.

Genetic Variation↗
PubMed1995

Structural study of the glycosylated and unglycosylated forms of a genetic variant of human serum albumin (63 Asp-->Asn).

A genetic variant of human serum albumin (alloalbumin) exhibited atypical electrophoretic mobility and chromatographic behavior apparently because of the effect of a point substitution on the molecular conformation. Three forms of albumin were isolated by DEAE HPLC chromatography: normal albumin, and two variant forms V1 and V2. The point substitution (Asp-63-->Asn) generated a canonical tripeptide acceptor sequence for glycosylation with an N-linked oligosaccharide (Asn-Lys-Ser). Neuraminidase digestion followed by electrophoresis showed that the V2 variant form was glycosylated and the V1 form was not. Time-of-flight mass spectrometry yielded a molecular weight of about 2000 for the carbohydrate. Structural analysis of the carbohydrate was done by chromatographic comparison of the pyridylaminated derivatives with standards and was confirmed by proton NMR of the three pronase glycopeptides and of the pyridylaminated oligosaccharide. The oligosaccharide had a complex biantennary structure with two sialic acid residues. In normal albumin Asp-63 is exposed and is adjacent to the first disulfide bond, Cys-62-->Cys-53. The apparent effect on molecular conformation resulting in incomplete glycosylation and atypical electrophoretic mobility suggests that glycosylation may interfere with disulfide bond formation at this site.

Amino Acid Sequence↗
PubMed2004

Interaction between a genetic variant of the platelet fibrinogen receptor and fibrinogen levels in determining the risk of cardiovascular events.

BACKGROUND: The PlA1A2 polymorphism of glycoprotein IIIa (GPIIIa), which affects postoccupancy signaling by the platelet fibrinogen receptor IIbIIIa, has been investigated as a potential genetic risk factor for cardiovascular events in numerous studies, without consistent results. We investigated whether the effect of this genetic variant of the platelet fibrinogen receptor on the risk of cardiovascular events is affected by fibrinogen plasma levels. METHODS: The GPIIIa PlA1A2 polymorphism and fibrinogen levels were determined in 455 men with angiographically documented coronary atherosclerosis. RESULTS: Neither carriership of the rare PlA2 allele nor fibrinogen plasma levels affected the time to cardiovascular event, as assessed in a proportional hazards model. However, there was a significant interaction between PlA2 carriership and fibrinogen plasma levels (P =.002). Carriership of the variant PlA2 allele significantly affected event-free survival only in individuals within the highest fibrinogen quartile (hazard ratio, 2.7; 95% CI, 1.1 to 7.1; P =.03). CONCLUSIONS: We observed a statistically significant interaction between a genetic variant of the platelet fibrinogen receptor and fibrinogen levels in determining the risk of cardiovascular events. This interaction may account for the inconsistent results of genetic association studies investigating this genotype as a genetic risk factor in thrombotic cardiovascular events.

Coronary Artery Disease↗
PubMed1998

Ligand specificity of the genetic variants of human alpha1-acid glycoprotein: generation of a three-dimensional quantitative structure-activity relationship model for drug binding to the A variant.

Human alpha1-acid glycoprotein (AAG) is a mixture of at least two genetic variants: the A variant and the F1 and/or S variant or variants, which are encoded by two different genes. In a continuation of previous studies indicating specific drug transport roles for each AAG variant according to its separate genetic origin, this work was designed to (1) determine the affinities of the two main gene products of AAG (i.e., the A variant and a mixture of the F1 and S variants) for 35 chemically diverse drugs and (2) to obtain meaningful 3D-QSARs for each binding site. Affinities were obtained by displacement experiments, leading to qualitative indications about binding site characteristics. In particular, drugs binding selectively to the A variant displayed some common structural features, but this was not seen for the F1*S variants. Three-dimensional QSAR analyses using the CoMFA method yielded a steric model for binding to the A variant, from which a simplified haptophoric model was derived. In contrast, no statistically sound model was found for the F1*S variants, possibly due (among other reasons) to an insufficient number of high affinity ligands in the set.

Alleles↗
PubMed1986

Fourteen genetically variant proteins of mouse brain: discovery of two new variants and chromosomal mapping of four loci.

With the description here of variant proteins A13 (pI 5.9, MW 62 kd) and A14 (pI 5.3, MW 26 kd), 14 polypeptides of mouse brain visualized by two-dimensional electrophoresis (2DE) exhibit genetic variation in isoelectric point. Using 22 B X D recombinant inbred strains, we map four of these loci and show that a fifth is independent of known loci. A pI 5.6, 81-kd protein of mouse brain mitochondria designated A1 is demonstrated to be an independent locus closely linked to LY-2 and LVP-1 on mouse chromosome 6. A pI 5.6, 28-kd genetically variant brain polypeptide designated A12 maps to chromosome 1 and shows identity with the known mouse locus LTW-4. The locus for A8 is not closely linked to any previously mapped locus. However, the locus for the newly described variant A13 shows 3 of 18 recombinants with the DNA polymorphism RN7S-2 and 2 of 18 recombinants with HC (hemolytic complement) and is thus probably located proximally to HC near the centromere of chromosome 2. Genetic and biochemical evidence is presented for the identification of A14 as ALP-1 (apolipoprotein 1), mapping to chromosome 9. In addition to these 13 genetically variant polypeptides, the positions of 12 other polypeptides which have been identified on 2DE gels of mouse brain are given.

Animals↗
PubMed1970

Absence of disulfide bonds linking the heavy and light chains: a property of a genetic variant of gamma-A2 globulins.

The gammaA2 globulins have attracted considerable interest because of the absence of the disulfide bonds linking the heavy and light chains characteristic of all other human immune globulins. Recently a genetic marker (Am(2)) has been found which delineates two genetic variants of gammaA2 globulins that are controlled by allelic genes. These differ markedly in incidence in different populations with a marked preponderance in Caucasians of the type possessing the Am(2) marker. A study of 22 gammaA2 myeloma proteins primarily from Caucasians showed that 20 were Am(2)(+), and 2 were Am(2)(-). All of the positive type dissociated in the presence of acid or urea into heavy and light chain dimers without reduction of disulfide bonds, as expected from the earlier studies. However, the two Am(2)(-) proteins failed to dissociate in the presence of acid, urea, guanidine, or detergent. It was only after partial reduction and alkylation that these molecules split into heavy and light chains. Thus the unique absence of disulfide bonds linking the heavy and light chains is a property of only one genetic variant and not of all gammaA2 proteins.

Chemistry Techniques, Analytical↗
PubMed2006

Common genetic variants in proinflammatory and other immunoregulatory genes and risk for non-Hodgkin lymphoma.

Profound disruption of immune function is an established risk factor for non-Hodgkin lymphoma. We report here a large-scale evaluation of common genetic variants in immune genes and their role in lymphoma. We genotyped 57 single nucleotide polymorphisms (SNP) from 36 candidate immune genes in 1,172 non-Hodgkin lymphoma cases and 982 population-based controls from a US multicenter study. We calculated odds ratios (OR) and 95% confidence intervals (95% CI) for the association between individual SNP and haplotypes with non-Hodgkin lymphoma overall and five well-defined subtypes. A haplotype comprising SNPs in two proinflammatory cytokines, tumor necrosis factor-alpha and lymphotoxin-alpha (rs1800629, rs361525, rs1799724, rs909253, and rs2239704), increased non-Hodgkin lymphoma risk overall (OR, 1.31; 95% CI, 1.06-1.63; P = 0.01) and notably for diffuse large B cell (OR, 1.64; 95% CI, 1.23-2.19; P = 0.0007). A functional nonsynonymous SNP in the innate immune gene Fc gamma receptor 2A (FCGR2A; rs1801274) was also associated with non-Hodgkin lymphoma; AG and AA genotypes were associated with a 1.26-fold (95% CI, 1.01-1.56) and 1.41-fold (95% CI, 1.10-1.81) increased risk, respectively (P(trend) = 0.006). Among non-Hodgkin lymphoma subtypes, the association with FCGR2A was pronounced for follicular and small lymphocytic lymphomas. In conclusion, common variants in genes influencing proinflammatory and innate immune responses were associated with non-Hodgkin lymphoma risk overall and their effects could vary by subtype. Our results require replication but potentially provide important clues for investigating common genetic variants as susceptibility factors and in disease outcomes, treatment responses, and immunotherapy targets.

Adult↗
PubMed2006

Genetic predisposition and renal allograft failure: implication of non-HLA genetic variants.

Renal allograft rejection or dysfunction often results in graft failure, and remains the major obstacle in the success of renal transplantation. Various immunological and nonimmunological factors are involved in allograft rejection. In addition to human leukocyte antigen loci, several genetically controlled molecules have been identified in recent years as playing important roles in the process of rejection. Genetic variants in genes encoding different T-helper (Th) type 1 and Th2 cytokines, chemokines and their receptors, growth factors, molecules of the renin-angiotensin system, enzymes of the homocysteine pathway, and proteins acting as substrates of immunosuppressive drugs impact on the success of engraftment and highlight the concept of genetic predisposition to allograft rejection. This review evaluates specific genetic variants and their functional roles in graft failure, with an emphasis on the latest methodologies available for genotyping, and appropriate strategies to enable them to become a tool of predictive and individualized medicine to ensure better transplant outcome.

Genetic Predisposition to Disease↗
PubMed2006

The significance of the hemochromatosis genetic variants in multiple myeloma in comparison to that of myelodysplastic syndrome.

The clinical experience of the significant difference in iron metabolism between multiple myeloma and myelodysplasia prompted us to analyse patients according to mutation frequency in the hemochromatosis gene (HFE) known to participate in the regulation of iron metabolism. HFE genotyping results were also evaluated in view of the clinical data in multiple myeloma (MM) patients. 49 patients with MM were compared to 61 patients with myelodysplastic syndrome (MDS) concerning the incidence of two genetic variants of the HFE gene (C282Y and H63D) identified with PCR-RFLP. Data of serum iron, transferrin saturation, consumed blood units and initial white blood cell counts (WBC) were analysed in relation to the HFE genotype status. 30 out of the 61 MDS patients (49%) and only 9 out of the 49 MM patients (20%) were positive for either HFE variant. Serum iron and transferrin saturation levels were all normal in MM and elevated in MDS patients. The initial WBC were significantly lower in the minority of MM patients who were at the same time heterozygous for the HFE gene variants. We found significant differences in the frequencies of the HFE genetic variants between MDS and MM patients with strong correlation to their iron metabolism. The low WBC in HFE positive MM patients unrelated to bone marrow infiltration rate might raise the suspicion of co-existent myelodysplasia.

Aged↗
PubMed2000

Identification of novel, functional genetic variants in the human matrix metalloproteinase-2 gene: role of Sp1 in allele-specific transcriptional regulation.

Matrix metalloproteinase-2 (MMP-2) is an enzyme with proteolytic activity against matrix and nonmatrix proteins, particularly basement membrane constituents. Thus, any naturally occurring genetic variants that directly affect gene expression and/or protein function would be expected to impact on progression of pathological processes involving tissue remodeling. We scanned a 2-kilobase pair promoter region and all 13 exons of the human MMP-2 gene, from a panel of 32 individuals, and we identified the position, nature, and relative allele frequencies of 15 variant loci as follows: 6 in the promoter, 1 in the 5'-untranslated region, 6 in the coding region, 1 in intronic sequence, and 1 in the 3'-untranslated region. The majority of coding region polymorphisms resulted in synonymous substitutions, whereas three promoter variants (at -1306, -790, and +220) mapped onto cis-acting elements. We functionally characterized all promoter variants by transient transfection experiments with 293, RAW264.7, and A10 cells. The common C --> T transition at -1306 (allele frequency 0.26), which disrupts an Sp1-type promoter site (CCACC box), displayed a strikingly lower promoter activity with the T allele. Electrophoretic mobility shift assays confirmed that these differences in allelic expression were attributable to abolition of Sp1 binding. These data suggest that this common functional genetic variant influences MMP-2 gene transcription in an allele-specific manner and is therefore an important candidate to test for association in a wide spectrum of pathologies for which a role for MMP-2 is implicated, including atherogenesis and tumor invasion and metastasis.

3' Untranslated Regions↗
PubMed1982

Functional assessment of genetic variants of alpha 1-antitrypsin.

The specific activity of thirteen genetic variants of the protease inhibitor alpha 1-antitrypsin (alpha 1AT) has been determined. Elastase inhibitor activity was assayed protein substrates (elastin and gelatin) and the synthetic substrate N-tert-butoxy-carbonyl-L-alanine p-nitrophenyl ester. The synthetic substrate alpha-N-benzoyl-DL-arginine p-nitroanilide HCl was used to assay trypsin inhibitor activity. The specific activity of alpha 1AT was expressed as serum inhibition/immunological concentration of alpha 1AT. Sera of PI type FM had reduced specific activity with elastase, but not with trypsin. With the possible exception of MP, no other variants showed significant differences in specific activity when compared with normal PI type M.

Elastin↗
PubMed1992

Genetic variants of alpha-1-antitrypsin (AAT).

This paper reviews the genetic variants of alpha-1-antitrypsin (AAT) which have been sequenced with special emphasis on the s.c. deficiency variants. These result in AAT low plasma levels via three main mechanisms: 1) intracellular storage; 2) intracellular degradation; 3) lack of synthesis. Intracellular storage occurs with the classical Z variant and with a few variants called M-like, because of their isoelectric focusing (IF) pattern. The storage phenomenon causes liver damage and can be demonstrated at both light and electron microscopic level with the help of immunohistochemistry. We report a new deficiency variant of AAT (M-Cagliari) characterized by very low plasma levels, massive storage of AAT and liver cirrhosis. By using immunohistochemical techniques and DNA analysis we could demonstrate that M-Cagliari has antigenic and genetic properties other than the Z AAT.

Base Sequence↗
PubMed2006

Health implications of milk containing beta-casein with the A2 genetic variant.

Milk from dairy cows has long provided a high quality source of protein and selected micronutrients such as calcium to most populations. Recently, a relationship between disease risk and consumption of a specific bovine ss-casein fraction either A1 or A2 genetic variants has been identified. Populations, which consume milk containing high levels of ss-casein A2 variant, have a lower incidence of cardiovascular disease and type 1 diabetes. Furthermore, consumption of milk with the A2 variant may be associated with less severe symptoms of autism and schizophrenia. The mechanism of action focuses on ss-casein A1 and related forms preferentially that are able to produce a bioactive opioid peptide, ss-casomorphin-7 (ss-CM-7) during digestion. Infants may absorb ss-CM-7 due to an immature gastrointestinal tract. Adults, on the other hand, appear to reap the biological activity locally on the intestinal brush boarder. ss-CM-7 can potentially affect numerous opioid receptors in the nervous, endocrine, and immune systems. Whether there is a definite health benefit to milk containing the A2 genetic variant is unknown and requires further investigation.

Adult↗