Missense mutations and single nucleotide polymorphisms in ABCB11 impair bile salt export pump processing and function or disrupt pre-messenger RNA splicing

Hepatology ◽  
2008 ◽  
Vol 49 (2) ◽  
pp. 553-567 ◽  
Author(s):  
Jane A. Byrne ◽  
Sandra S. Strautnieks ◽  
Gudrun Ihrke ◽  
Franco Pagani ◽  
A.S. Knisely ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Bile Salt ◽  
Rna Splicing ◽  
Messenger Rna ◽  
Missense Mutations ◽  
Nucleotide Polymorphisms ◽  
Bile Salt Export Pump ◽  
Single Nucleotide ◽  
And Function

scholarly journals Polymorphisms in the Chicken Growth Differentiation Factor 9 Gene Associated with Reproductive Traits

2018 ◽  
Vol 2018 ◽  
pp. 1-11 ◽  
Author(s):  
Lingbin Liu ◽  
Zhifu Cui ◽  
Qihai Xiao ◽  
Haihan Zhang ◽  
Xiaoling Zhao ◽  
...  
Keyword(s):  
Body Weight ◽  
Single Nucleotide Polymorphisms ◽  
Gene Polymorphisms ◽  
Reproductive Traits ◽  
Missense Mutations ◽  
Nucleotide Polymorphisms ◽  
Rt Pcr ◽  
Single Nucleotide ◽  
Egg Weight ◽  
Growth Differentiation Factor 9

The aim of the study was to investigateGDF9gene polymorphisms and their association with reproductive traits in chicken using DNA sequencing. A total of 279 Dongxiang blue-shelled (DX) chickens and 232 Luhua (LH) chickens were used for validation. We detected 15 single nucleotide polymorphisms (SNPs): nine SNPs were previously unreported in chicken, two were missense mutations, and only three exhibited significant associations with reproductive traits. G.17156387C>T was significantly associated with age at first egg (AFE) and weight of first egg (WFE) in both breeds. Birds carrying the CC genotype exhibited higher AFE and WFE values than those with the TT genotype. The SNP g.17156427A>G exhibited an association with egg weight at 300 days of age (EWTA) in DX but not in LH chickens. The SNP g.17156703A>C affected the AFE and EN (total number of eggs at 300 days of age) in DX chickens. In addition, certain diplotypes significantly affected AFE, BWTA (body weight at 300 days of age), and EN in both breeds. RT-PCR results showed that theGDF9gene was highly expressed in stroma with cortical follicles (STR) and prehierarchal follicles. These results provided further evidence that theGDF9gene is involved in determining reproductive traits in chicken.

Single nucleotide polymorphisms (SNPs) in human lactoferrin geneThis paper is one of a selection of papers published in this Special Issue, entitled 7th International Conference on Lactoferrin: Structure, Function and Applications, and has undergone the Journal's usual peer review process.

2006 ◽  
Vol 84 (3) ◽  
pp. 381-384 ◽  
Author(s):  
Christina T. Teng ◽  
Wesley Gladwell
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Inflammatory Responses ◽  
Peer Review Process ◽  
Genome Project ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Environmental Health Sciences ◽  
Normal Healthy Individual ◽  
Lactoferrin Gene ◽  
And Function

The lactoferrin protein possesses antimicrobial and antiviral activities. It is also involved in the modulation of the immune response. In a normal healthy individual, lactoferrin plays a role in the front-line host defense against infection and in immune and inflammatory responses. Whether genomic variations, such as single nucleotide polymorphisms (SNPs), have an effect on the structure and function of lactoferrin protein and whether these variations contribute to the different susceptibility of individuals in response to environmental insults are interesting health-related issues. In this study, the lactoferrin gene was resequenced as part of the Environmental Genome Project of the National Institute of Environmental Health Sciences, which operates within the National Institutes of Health. Ninety-one healthy donors of different ethnicities were used to establish common SNPs in the exons of the lactoferrin gene in the general population. The data will serve as a basis from which study the association of lactoferrin polymorphism and disease.

In Silico Analysis of Non Synonymous Single Nucleotide Polymorphisms (nsSNPs) of SMPX Gene in Hearing Impairment

2018 ◽  
Author(s):  
Md. Arifuzzaman ◽  
Sarmistha Mitra ◽  
Amir Hamza ◽  
Raju Das ◽  
Nurul Absar ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Protein Stability ◽  
In Silico Analysis ◽  
Normal Activity ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Binding Motifs ◽  
Stability Change ◽  
And Function ◽  
Dbsnp Database

ABSTRACTBackgroundMutations in SMPX gene can disrupt the normal activity of the SMPX protein which is involved in hearing process.ObjectiveIn this study, deleterious non-synonymous single nucleotide polymorphisms were isolated from the neutral variants by using several bioinformatics tools.MethodFirstly, dbSNP database hosted by NCBI was used to retrieve the SNPs of SMPX gene, secondly, SIFT was used primarily to screen the damaging SNPs. Further, for validation PROVEAN, PredictSNP and PolyPhen 2 were used. I-Mutant 3 was utilized to analyze the protein stability change and MutPred predicted the molecular mechanism of protein stability change. Finally evolutionary conservation was done to study their conservancy by using ConSurf server.ResultsA total of 26 missense (0.6517%) and 3 nonsense variants (0.075%) were retrieved and among them 4 mutations were found deleterious by all the tools of this experiment and are also highly conserved according to ConSurf server. rs772775896, rs759552778, rs200892029 and rs1016314772 are the reference IDs of deleterious mutations where the substitutions are S71L, N19D, A29T and K54N. Loss of Ubiquitination, loss of methylation, loss of glycosylation, and loss of MoRF binding motifs are the root causes of protein stability change.ConclusionThis is the first study regarding nsSNPs of SMPX gene where the most damaging SNPs were screened that are associated with the SMPX gene and can be used for further research to study their effect on protein structure and function, their dynamic behavior and how they actually affect protein’s flexibility.

scholarly journals Susceptibility of the Iranian population to severe acute respiratory syndrome coronavirus 2 infection based on variants of angiotensin I converting enzyme 2

2020 ◽  
Vol 15 (8) ◽  
pp. 507-514
Author(s):  
Alireza Mohebbi ◽  
Fatemeh Sana Askari ◽  
Mohsen Ebrahimi ◽  
Mana Zakeri ◽  
Mohammad Yasaghi ◽  
...  
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Single Nucleotide Polymorphisms ◽  
Resistance Mutation ◽  
Iranian Population ◽  
Natural Resistance ◽  
Missense Mutations ◽  
Nucleotide Polymorphisms ◽  
Converting Enzyme ◽  
Viral Glycoprotein ◽  
Single Nucleotide

Background: Variations in the viral receptor human angiotensin-converting enzyme 2 (ACE2) may specify the susceptibility of a certain population to severe acute respiratory syndrome coronavirus 2. Objective: Evaluation of the affinity of severe acute respiratory syndrome coronavirus 2 spike glycoprotein to the Iranian genetic variants of ACE2. Materials & methods: Single nucleotide polymorphisms of ACE2 among the Iranian population were collected from the Iranome database. Missense mutations in the N-terminal peptidase domain were selected for in silico analysis. Results: 17 missense single nucleotide polymorphisms were found at ACE2. Viral glycoprotein had the lowest affinity to ACE2 mutant V485L. Discussion: The V485L variant of ACE2 could be a natural resistance mutation among the Iranian population. In addition, variant S331F can increase slightly the susceptibility to infection with the virus.

Association of MALAT-1 gene single nucleotide polymorphisms with genetic susceptibility to systemic lupus erythematosus

Lupus ◽  
2021 ◽  
pp. 096120332110403
Author(s):  
Yan-Mei Mao ◽  
Yi-Sheng He ◽  
Guo-Cui Wu ◽  
Yu-Qian Hu ◽  
Kun Xiang ◽  
...  
Keyword(s):  
Systemic Lupus Erythematosus ◽  
Single Nucleotide Polymorphisms ◽  
Lupus Erythematosus ◽  
Clinical Characteristics ◽  
Clinical Manifestations ◽  
Additive Models ◽  
Nucleotide Polymorphisms ◽  
Systemic Lupus ◽  
Single Nucleotide ◽  
And Function

Background: Abnormal expression and function of long non-coding RNAs (lncRNAs) are closely related to the pathogenesis of systemic lupus erythematosus (SLE). In this study, we aimed to investigate the association of lncRNA metastasis-associated lung adenocarcinoma transcript 1 (MALAT-1) gene single-nucleotide polymorphisms (SNPs) with susceptibility and clinical characteristics of SLE patients. Methods: A case-control study including 489 SLE patients and 492 healthy controls was conducted. Four MALAT-1 SNPs (rs4102217, rs591291, rs11227209, and rs619586) were genotyped in all subjects, their correlation with SLE susceptibility and clinical characteristics were also analyzed. Results: Results showed that the rs4102217 locus was associated with the risk of SLE. In recessive models, the GG+CG genotype of rs4102217 was associated with the decreased risk of SLE compared to CC ( p = 0.036, OR = 0.348, 95% CI: 0.124–0.975). In additive models, the GG genotype of rs4102217 was associated with the decreased risk of SLE compared to CC ( p = 0.040, OR = 0.355, 95% CI: 0.127–0.996). However, no association was found between MALAT-1 gene polymorphism and clinical manifestations of SLE (all p > 0.05). Conclusion: In summary, MALAT-1 rs4102217 is associated with susceptibility to SLE, suggesting that MALAT-1 may play a role in SLE.

scholarly journals Sarcopenia, Obesity, and Sarcopenic Obesity: Relationship with Skeletal Muscle Phenotypes and Single Nucleotide Polymorphisms

2021 ◽  
Vol 10 (21) ◽  
pp. 4933
Author(s):  
Praval Khanal ◽  
Alun G. Williams ◽  
Lingxiao He ◽  
Georgina K. Stebbings ◽  
Gladys L. Onambele-Pearson ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Single Nucleotide Polymorphisms ◽  
Biceps Brachii ◽  
Muscle Quality ◽  
Sarcopenic Obesity ◽  
Gene Variants ◽  
Nucleotide Polymorphisms ◽  
Obese Women ◽  
Single Nucleotide ◽  
And Function

Obesity may aggravate the effects of sarcopenia on skeletal muscle structure and function in the elderly, but no study has attempted to identify the gene variants associated with sarcopenia in obese women. Therefore, the aims of the present study were to: (1) describe neuromuscular function in sarcopenic and non-sarcopenic women with or without obesity; (2) identify gene variants associated with sarcopenia in older obese women. In 307 Caucasian women (71 ± 6 years, 66.3 ± 11.3 kg), skeletal muscle mass was estimated using bioelectric impedance, and function was tested with a 30 s one-leg standing-balance test. Biceps brachii thickness and vastus lateralis cross-sectional area (VLACSA) were measured with B-mode ultrasonography. Handgrip strength, maximum voluntary contraction elbow flexion (MVCEF), and knee extension torque (MVCKE) were measured by dynamometry, and MVCKE/VLACSA was calculated. Genotyping was performed for 24 single-nucleotide polymorphisms (SNPs), selected based on their previous associations with muscle-related phenotypes. Based on sarcopenia and obesity thresholds, groups were classified as sarcopenic obese, non-sarcopenic obese, sarcopenic non-obese, or non-sarcopenic non-obese. A two-way analysis of covariance was used to assess the main effects of sarcopenia and obesity on muscle-related phenotypes and binary logistic regression was performed for each SNP to investigate associations with sarcopenia in obesity. There were no significant obesity * sarcopenic status interactions for any of the investigated muscle-related phenotypic parameters. Neither sarcopenia nor obesity had a significant effect on biceps brachii thickness, but sarcopenia was associated with lower VLACSA (p = 0.003). Obesity was associated with lower MVCEF (p = 0.032), MVCKE (p = 0.047), and MVCKE/VLACSA (p = 0.012) with no significant effect of sarcopenia. Adjusted for age and height, three SNPs (ACTN3 rs1815739, MTHFR rs1801131, and MTHFR rs1537516) were associated with sarcopenia in obese participants. Sarcopenia was associated with a smaller muscle size, while obesity resulted in a lower muscle quality irrespective of sarcopenia. Three gene variants (ACTN3 rs1815739, MTHFR rs1801131, and MTHFR rs1537516) suspected to affect muscle function, homocysteine metabolism, or DNA methylation, respectively, were associated with sarcopenia in obese elderly women. Understanding the skeletal muscle features affected by sarcopenia and obesity, and identification of genes related to sarcopenia in obese women, may facilitate early detection of individuals at particular risk of sarcopenic obesity.

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