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.

SourceResearch connectionFrom yearThrough year

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

At least 253 records · Page 14Linked to original sources

PubMed2025

Contributions of Common, Rare, and Somatic Genetic Variants to Incidence of Atrial Fibrillation.

IMPORTANCE: Atrial fibrillation (AF) has a complex genetic architecture involving common, rare, and somatic variants. The association between these components requires further investigation. OBJECTIVE: To examine the individual and combined contributions of polygenic, monogenic, and somatic genetic variants to AF incidence, and develop an integrated genomic model (IGM-AF) for improved risk prediction. DESIGN, SETTING, AND PARTICIPANTS: This cohort study used whole-genome sequence data from participants of the UK Biobank, with follow-up for AF events through hospital records, death registries, and self-report. The UK Biobank recruited participants aged 40 to 69 years in the UK between 2006 and 2010. Study data were analyzed from August 2022 to November 2024. EXPOSURES: IGM-AF comprising an AF polygenic risk score (PRS), a composite rare variant gene set (AFgeneset), and somatic variants associated with clonal hematopoiesis of indeterminate potential (CHIP). Clinical AF risk was estimated using the Cohorts for Heart and Aging Research in Genomic Epidemiology AF (CHARGE-AF) score. MAIN OUTCOMES AND MEASURES: The primary outcome was hazard ratios (HRs) for 5-year incident AF attributable to PRS, AFgeneset, CHIP, and their interactions. The predictive performance of IGM-AF and its components was quantified using HRs, C statistics, and reclassification indices. RESULTS: A total of 416 085 individuals (mean [SD] age, 56.6 [8.0] years; 224 642 female [54.0%]) with 30 797 AF cases were included. The PRS (HR per 1 SD, 1.65; 95% CI, 1.63-1.67; P < 1 × 10-8), AFgeneset (HR, 1.63; 95% CI, 1.52-1.75; P = 1.46 × 10-42), and CHIP (HR, 1.26; 95% CI, 1.15-1.38; P = 1.41 × 10-6) were associated with incident AF. The 5-year cumulative incidence of AF was at least 2-fold among individuals having all 3 genetic drivers (common, rare, and somatic drivers) compared with those with only 1 driver. Integration of IGM-AF with a clinical risk model (CHARGE-AF) showed higher predictive performance (C statistic, 0.80; 95% CI, 0.80-0.80) compared with IGM-AF and CHARGE-AF alone. The classification of the at-risk population for AF was improved when IGM-AF was added to CHARGE-AF (net reclassification index, 0.08; 95% CI, 0.07-0.09). CONCLUSIONS AND RELEVANCE: Results of this cohort study demonstrated the complementary value of common, rare, and somatic variants in shaping genomic AF risk. Leveraging comprehensive genetic information may enhance screening and preventive interventions for AF.

Humans↗

PubMed2002

Genetic variants of NHEJ DNA ligase IV can affect the risk of developing multiple myeloma, a tumour characterised by aberrant class switch recombination.

The DNA double stranded break (DSB) repair mechanism, non-homologous end joining (NHEJ) represents an essential step in antigen receptor gene rearrangement mechanisms, processes believed to be intimately involved in the aetiology of lymphoproliferative disease. We investigated the potential impact that previously undescribed polymorphisms identified within NHEJ DNA ligase IV (LIG4) have upon predisposition to several lymphoproliferative disorders, including leukaemia, lymphoma, and multiple myeloma. Two LIG4 polymorphisms were examined, both C>T transitions, which result in the amino acid substitutions A3V and T9I. Inheritance of the LIG4 A3V CT genotype was found to be significantly associated with a two-fold reduction in risk of developing multiple myeloma (OR 0.49, 95% CI 0.27 to 0.89). Similarly, inheritance of the LIG4 T9I CT and the T9I TT genotypes were found to associate with a 1.5-fold reduction (OR 0.77, 95% CI 0.51 to 1.17) and a four-fold reduction (OR 0.22, 95% CI 0.07 to 0.70) in risk of developing multiple myeloma respectively, suggesting a gene dosage effect for this polymorphism. The LIG4 A3V and T9I variant alleles are in linkage disequilibrium (D'=0.95, p<0.0001), and the protective effect associated with these polymorphisms was found to be the result of inheritance of the A3V-T9I CT and A3V-T9I TT haplotypes. These data suggest that genetic variants of NHEJ LIG4 may modulate predisposition to multiple myeloma, a tumour characterised by aberrant immunoglobulin (Ig) class switch recombination.

Base Sequence↗

PubMed2006

Genetic variants in the glucocorticoid receptor gene (NR3C1) and cardiovascular disease risk. The Leiden 85-plus Study.

Recently, the ER22/23EK, N363S and BclI polymorphisms in the glucocorticoid receptor (GR) gene have been linked to altered cortisol sensitivity and to cortisol-associated disorders. The aim of this study was to investigate the effect of these genetic variants in the GR gene on cardiovascular disease and mortality in elderly persons aged 85 years and over. In the population-based Leiden 85-plus Study, 552 participants were genotyped for the ER22/23EK, N363S and BclI polymorphisms, and the effects of the polymorphisms on metabolic profile, body composition, and on the prevalence of cardiovascular pathologies at baseline, were assessed. Allcause and cardiovascular disease mortality risks dependent on the SNPs were calculated after a 4.2-year follow-up. The analyses of metabolic profile revealed that carriers of the ER22/23EK polymorphism have higher HbA1C levels (P<0.001) and carriers of the N363S SNP have higher LDL cholesterol (P<0.001) and triglyceride concentrations (P=0.03), compared to the non-carriers. The only significant association between genotype and body composition analyses was for height and the ER22/23EK polymorphism. Men carrying the ER22/23EK polymorphism were taller (P=0.02) compared to non-carriers. No associations with cardiovascular pathologies, allcause and cardiovascular mortality were observed for any of the polymorphisms. We conclude that, in spite the effect of the ER22/23EK and N363S SNPs on metabolism, these polymorphisms together with the BclI SNP, do not affect the risks of cardiovascular disease and survival at old age.

Age Distribution↗

PubMed1986

Genetic variants detected among 106 lymphocyte polypeptides observed in two-dimensional gels.

Peripheral blood lymphocytes from 40 children have been examined for genetic variation in their protein constituents by two-dimensional polyacrylamide gel electrophoresis. One hundred six polypeptides chosen without respect to genetic variability were scored in gels from the 40 children. For each child, gels from both parents were also examined to substantiate the genetic basis of variants observed. Of the total of 4,240 polypeptides, 23 could not be scored unambiguously. Fourteen of the polypeptides showed genetic variants in one or more of the children. One hundred twenty-nine of 4,217 polypeptides scored exhibited the combination of a normal and a variant polypeptide. All variants were present in at least one of the parents of the subject. The index of heterozygosity observed (3.05% +/- .23%) indicates substantial genetic variation in cellular protein constituents.

Adult↗

PubMed2005

Genetic variants in nonclassical major histocompatibility complex class I human leukocyte antigen (HLA)-E and HLA-G molecules are associated with susceptibility to heterosexual acquisition of HIV-1.

Human leukocyte antigen (HLA)-E and HLA-G molecules act as powerful modulators of the innate immune response. The present study shows that the HLA-E(G) genetic variant (the HLA-E*0103 allele) alone is significantly (P = .001) associated with a 4.0-fold decreased risk of human immunodeficiency virus 1 (HIV-1) infection in Zimbabwean women. Furthermore, women carrying the combination of the protective HLA-E(G) homozygote and HLA-G*0105N heterozygote genotypes had a 12.5-fold decreased risk of HIV-1 infection (P = .03), compared with women carrying neither genotype. These associations remained significant after adjustment was made for other significant sociodemographic risk factors for HIV prevalence in this population. In conclusion, HLA-E and HLA-G polymorphisms can independently and synergistically influence susceptibility to heterosexual acquisition of HIV-1.

Female↗

PubMedDate not supplied

[A new genetic variant of the PUUV virus from the Maritime Territory and its natural carrier red-grey vole Clethrionomys rufocanus].

Pulmonary tissues of red-grey voles, Clethrionomys rufocanus from Shkotovo District and Maritime Territory were investigated. rt-PCR was used to detect the hantavirus nt-222 M-segment genome and nt-403 mitochondrial DNA fragment. A new genetic variant of the PUUV virus named as "Shkotovo", that is different from other PUUV strains by 18-23%, was shown to be circulating in red-grey voles. A phylogenetic analysis denoted 2 PUUV subgroups with their rodent-host branching into C. graleolus and C. rufocanus.

Amino Acid Sequence↗

PubMed2002

Genetic variant of the histamine-1 receptor (glu349asp) and body weight change during clozapine treatment.

Clozapine treatment frequently causes body weight gain that may impair health and may affect patient compliance. While the histamine-1 (H1) receptor may play a major role in the mechanism of the clozapine-induced body weight change, we tested the relationship between the genetic variant (Glu349Asp) of the H1 receptor and the clozapine-induced body weight change. Eighty-eight schizophrenic patients treated with clozapine were included in this study. Analysis of body weight change after 4 months of clozapine treatment showed no relationship with the H1 genotype. Further exploration of the other H1 genotypes and the antipsychotic-induced body weight change may help in the understanding of the mechanisms of antipsychotic-induced body weight gain and in the choice of patient's antipsychotic regimens.

Adolescent↗

PubMed2006

Genetic variants in matrix metalloproteinase genes are associated with development of gastric ulcer in H. Pylori infection.

BACKGROUND AND AIMS: Matrix metalloproteinases (MMPs) are a family of enzymes that degrade most of the macromolecules making up the extracellular matrix. H. pylori infection increases the secretion of MMPs in the gastric mucosa leading to severe mucosal damage. The aim of this study was to investigate if genetic variants in MMPs involved in the inflammatory response to H. pylori could predispose patients with chronic H. pylori infection to develop gastric ulcer disease. METHODS: A total of 599 H. pylori-infected patients undergoing gastroscopy were genotyped for 20 SNPs covering the MMP-1, -3, -7, and -9 genes by TaqMan technology. Haplotype and single marker analysis was conducted to assess associations with gastric ulcer disease. RESULTS: Carriage of allele G of the functional promoter variant MMP-7-181 was significantly associated with gastric ulcer conferring a 1.6-fold increased risk (95% CI: 1.0-2.6, p = 0.037). In addition, carriage of allele A of a coding SNP in exon 6 of MMP-9 confers a 2.4-fold increased risk (95% CI: 1.0-2.6, p = 0.013) for gastric ulcer. CONCLUSION: The level of association found in this study is in agreement with the nature of a complex genetic disease. Genetic variations in the MMP-7 and -9 gene may be part of a complex genetic risk profile to develop gastric ulcer in chronic H. pylori infection. Further studies are warranted to elucidate the pathophysiological role of these genes in ulcerogenesis.

Base Sequence↗

PubMed2003

Pathogenic potential of environmental Vibrio cholerae strains carrying genetic variants of the toxin-coregulated pilus pathogenicity island.

The major virulence factors of toxigenic Vibrio cholerae are cholera toxin (CT), which is encoded by a lysogenic bacteriophage (CTXPhi), and toxin-coregulated pilus (TCP), an essential colonization factor which is also the receptor for CTXPhi. The genes for the biosynthesis of TCP are part of a larger genetic element known as the TCP pathogenicity island. To assess their pathogenic potential, we analyzed environmental strains of V. cholerae carrying genetic variants of the TCP pathogenicity island for colonization of infant mice, susceptibility to CTXPhi, and diarrheagenicity in adult rabbits. Analysis of 14 environmental strains, including 3 strains carrying a new allele of the tcpA gene, 9 strains carrying a new allele of the toxT gene, and 2 strains carrying conventional tcpA and toxT genes, showed that all strains colonized infant mice with various efficiencies in competition with a control El Tor biotype strain of V. cholerae O1. Five of the 14 strains were susceptible to CTXPhi, and these transductants produced CT and caused diarrhea in adult rabbits. These results suggested that the new alleles of the tcpA and toxT genes found in environmental strains of V. cholerae encode biologically active gene products. Detection of functional homologs of the TCP island genes in environmental strains may have implications for understanding the origin and evolution of virulence genes of V. cholerae.

Animals↗

PubMed2003

Genetic variants of endothelial nitric oxide synthase in patients with primary biliary cirrhosis: association with disease severity.

BACKGROUND AND AIMS: Primary biliary cirrhosis (PBC) presents a wide spectrum of clinical manifestations. In experimental models of liver cirrhosis and cholestasis it has been suggested that altered nitric oxide production is involved in liver injury and portal hypertension development. The present study investigated endothelial nitric oxide synthase (eNOS) genetic polymorphisms (894G/T, -786T/C) in patients with PBC and in controls to verify whether disease susceptibility and progression are associated with a particular genotype. METHODS: Genomic DNA from 109 Italian PBC patients (65 with advanced disease, i.e. liver transplantation or histological stage III-IV) was obtained and polymorphisms determined by fluorescent probe analysis. Healthy subjects (n = 242) were used as a control group. RESULTS: The allelic frequencies of both polymorphisms did not differ significantly between PBC patients and controls. When the association between genotypes and disease severity was addressed, both the 894T and the -786T alleles were more frequently found in the 22 patients with progressing disease (894T, frequency 0.455 compared with 0.240; P = 0.032; -786T, frequency 0.682 compared with 0.460; P = 0.038). Patients with 894TT presented higher Mayo score values (6.1 +/- 1.2 compared with 5.4 +/- 1.3 in 894G/G patients; P = 0.030) but similar age and disease duration values. CONCLUSIONS: The authors suggest that genetic variants of eNOS are not associated with susceptibility to PBC, although the genotypes may lead to differences in disease severity and progression.

Adult↗

PubMed1989

Genetic variants of chronic granulomatous disease: prevalence of deficiencies of two cytosolic components of the NADPH oxidase system.

Chronic granulomatous disease, a syndrome of recurrent infections and failure of oxidative microbicidal activity in phagocytes, results from defects in the gene for one of several components of an oxidase system that can undergo activation. To determine the relative prevalence of certain of the genetic variants of this disorder, we used immunoblotting to detect two specific neutrophil cytosolic proteins of 47 and 67 kd recently shown to be required for oxidase activation. Chronic granulomatous disease is usually an X-linked disorder associated with the absence of membrane cytochrome b558. Of our 94 patients with chronic granulomatous disease, however, 36 had a phenotype characterized by autosomal inheritance, normal membrane oxidase components (including cytochrome b558), and functionally defective cytosolic activity in a cell-free oxidase system. We studied 25 of these 36 patients and found that 22 lacked the 47-kd cytosolic protein, and the remaining 3 were missing the 67-kd component. Patients with chronic granulomatous disease whose functional defect was localized to the neutrophil membrane (classic X-linked cytochrome b-negative type and two other rare variants) had normal amounts of both cytosolic components. We estimate that approximately 33 percent of all patients with chronic granulomatous disease are missing the 47-kd cytosolic oxidase component and about 5 percent of patients are missing the 67-kd component. Chronic granulomatous disease caused by a defect in any cytosolic factors other than the 47-kd and 67-kd proteins, if it exists, is apparently rare.

Adolescent↗

PubMed2006

Genetic variants in the promoter region of the IGF-I gene as a reason for short stature.

DNA obtained from the blood cells of 88 adolescent patients with short stature, with low blood serum IGF-I concentrations, normal growth hormone (GH) secretion and normal GH receptor (GHR) structure, was analyzed in the promoter region for the IGF-I gene. A total of 24 genetic variants was detected in the DNA of 13 patients. An attempt was also made to analyze the impact of identified mutations on DNA-protein interactions using EMSA.

5' Untranslated Regions↗

PubMed1978

Structural comparison of glycophorins and immunochemical analysis of genetic variants.

Differences in amino acid sequence of erythrocyte membrane glycophorin A are correlated with M or N blood group activity. A second sialoglycoprotein, glycophorin B, has an amino acid sequence identical to that of glycophorin AN in the first 23 positions and carries N activity only, suggesting that different structural genes code for the glycoproteins carrying these antigens. Certain genetically variant cells lack glycophorin A, as determined by immunochemical methods, and serological MN activity. Other variants lack MN activity, but contain normal amounts of glycophorin A in the membrane.

Amino Acid Sequence↗

PubMed2003

Differential degradation of amyloid beta genetic variants associated with hereditary dementia or stroke by insulin-degrading enzyme.

Inherited amino acid substitutions at position 21, 22, or 23 of amyloid beta (Abeta) lead to presenile dementia or stroke. Insulin-degrading enzyme (IDE) can hydrolyze Abeta wild type, yet whether IDE is capable of degrading Abeta bearing pathogenic substitutions is not known. We studied the degradation of all of the published Abeta genetic variants by recombinant rat IDE (rIDE). Monomeric Abeta wild type, Flemish (A21G), Italian (E22K), and Iowa (D23N) variants were readily degraded by rIDE with a similar efficiency. However, proteolysis of Abeta Dutch (E22Q) and Arctic (E22G) was significantly lower as compared with Abeta wild type and the rest of the mutant peptides. In the case of Abeta Dutch, inefficient proteolysis was related to a high content of beta structure as assessed by circular dichroism. All of the Abeta variants were cleaved at Glu3-Phe4 and Phe4-Arg5 in addition to the previously described major sites within positions 13-15 and 18-21. SDS-stable Abeta dimers were highly resistant to proteolysis by rIDE regardless of the variant, suggesting that IDE recognizes a conformation that is available for interaction only in monomeric Abeta. These results raise the possibility that upregulation of IDE may promote the clearance of soluble Abeta in hereditary forms of Abeta diseases.

Amyloid beta-Peptides↗

PubMed2006

Genetic variants of UGT1A6 influence risk of colorectal adenoma recurrence.

PURPOSE: The UDP glucuronosyltransferase 1A6 (UGT1A6) and cytochrome P450 2C9 (CYP2C9) enzymes participate in the metabolism of nonsteroidal anti-inflammatory drugs, endogenous substances, and carcinogens. Functional polymorphisms of UGT1A6 (T181A and R184S) and CYP2C9 (R144C and I359L) have been reported to modify the protective effect of aspirin on colorectal adenoma risk. We aimed to further investigate the effect of these genetic variants on the development of colorectal neoplasia. EXPERIMENTAL DESIGN: We examined the relationship between UGT1A6 and CYP2C9 genotype and colorectal adenoma recurrence in 546 patients participating in a randomized placebo-controlled aspirin intervention trial. RESULTS: Although colorectal adenoma recurrence was not significantly influenced by CYP2C9 genotype, carriers of variant UGT1A6 alleles were at significantly reduced risk of colorectal neoplasia recurrence [relative risk (RR), 0.68; 95% confidence interval (95% CI), 0.52-0.89]. This risk reduction was also evident when the analysis was confined to advanced neoplasia recurrence (RR, 0.71; 95% CI, 0.47-1.09). When patients were stratified by genotype and aspirin intervention, those with variant UGT1A6 alleles were at reduced recurrence risk irrespective of whether they received aspirin or placebo (RR, 0.62; 95% CI, 0.42-0.92 and RR, 0.63; 95% CI, 0.44-0.91, respectively). CONCLUSIONS: These findings confirm that UGT1A6 variants influence colorectal carcinogenesis independent of aspirin intake and suggest that they may have clinical value in secondary prevention programs for patients diagnosed with colorectal adenoma.

Adenoma↗

PubMed2005

A genetic variant c.553G > T in the apolipoprotein A5 gene is associated with an increased risk of coronary artery disease and altered triglyceride levels in a Chinese population.

Elevation in plasma triglycerides (TG) has been widely accepted as a coronary artery disease (CAD) risk predictor. Recently, a new apolipoprotein playing an important role in TG metabolism named apolipoprotein AV (apoAV) was discovered, which is encoded by the APOA5 gene. Several single nucleotide polymorphisms (SNPs) of APOA5 associated with increased TG concentrations have been identified. We here report that a recently identified genetic variant, c.553G>T in the APOA5 gene which causes a substitution of a cysteine for a glycine residue at amino acid residue 185(G185C) is also associated with increased TG levels. To investigate the association between this genetic variation and the risk of CAD, a case-control study comprising 232 patients with CAD and 302 controls from the same area of China was performed. The minor allele frequencies of c.553G > T for the CAD and control groups were 7.76 and 3.97%, respectively (P = 0.008). In both the CAD and control groups, the T allele carriers had higher serum TG levels than homozygous carriers of the major G allele (CAD group: 2.67 +/- 1.48 mmol/l versus 1.95 +/- 1.02 mmol/l, P = 0.021; controls: 2.31 +/- 1.20 mmol/l versus 1.68 +/- 0.95 mmol/l, P = 0.002). After adjustment for age, gender, body mass index, smoking status, glucose and presence of hypertension, the odds ratio (OR) for CAD in the T allele carriers was 2.089 (95% CI = 1.140-3.830, P = 0.017), in comparison to the individuals without the T allele. These results suggest that the APOA5 c.553G > T polymorphism is an important predictor for hypertriglyceridemia and CAD.

Amino Acid Substitution↗

PubMedDate not supplied

Genetic variants of hepatocyte nuclear factor-1beta in Chinese young-onset diabetic patients with nephropathy.

In Hong Kong, the prevalence of diabetes is estimated to be 2% in the young population. In the diabetic population, 30% of patients have diagnosis before the age of 40 years. Besides, 30% of young diabetic patients have varying degrees of albuminuria. Mutations in the gene encoding the hepatocyte nuclear factor (HNF)-1beta are associated with a subtype of maturity-onset diabetes of the young (MODY 5) characterized by urogenital abnormalities. We examined 74 unrelated Chinese subjects with young-onset diabetes complicated by nephropathy for variants in this gene. The HNF-1beta gene was screened by direct sequencing and the functional properties of wild-type and mutant proteins were analyzed by transactivation analysis.A novel variant in exon 3 (E260D) was found in one patient. Extended family analysis revealed four other siblings carrying this variant. One subject had diabetes and another had impaired glucose tolerance. Another sibling had microalbuminuria but normal glucose tolerance. Transfection studies showed insignificant differences in transactivation ability between wild-type and mutated HNF-1beta. A silent polymorphism Q378Q was identified in another unrelated subject. These results suggest genetic variants in HNF-1beta are not a common cause of young-onset diabetes or diabetic nephropathy in Chinese, but may modify disease manifestation and progression. Other potential candidate genes should be looked for to account for the high prevalence of young-onset diabetes and nephropathy in this population.

Adolescent↗

PubMed2005

Genetic variants of transferrin in the diagnosis of protein hypoglycosylation.

Human transferrin (Tf) shows genetic polymorphisms, which may interfere in the screening of congenital disorders of glycosylation (CDG). Isoelectric focusing followed by direct immunofixation was used for Tf analysis in controls and several groups of patients. Equivocal results in one case have been recognized as a rare Tf CD variant. A higher incidence of some genetic variants has been reported in connection with certain diseases; of the seven Tf phenotypes detected in our set of samples, an apparently higher frequency of Tf C1C2 variant found in some groups of patients was not significant.

Adolescent↗