Deciphering the association of intronic single nucleotide polymorphisms of crystallin gene family with congenital cataract

Nair, Vidya; Sankaranarayanan, Rajkumar; Vasavada, Abhay R.

doi:10.4103/ijo.ijo_3062_20

Cited by 18 publications

(6 citation statements)

References 42 publications

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“…The functional role of the genomic region strongly determines the localization of polymorphisms, since SNPs in exons have a potential impact on gene products that on a further scope may be the cause of a disease or may alter quantitative phenotypes (15). Since introns exhibit various regulatory roles, the presence of polymorphism in introns may indirectly impact gene products or their expression levels (16).…”

Section: Discussionmentioning

confidence: 99%

Exploring the Distribution of Single Nucleotide Polymorphisms Across Human Exons and Introns

Fraszczak,

Liu,

Mielczarek

et al. 2024

Preprint

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Among all types of mutations, single nucleotide polymorphisms are the most common type of genomic variation. In our study, we explore the counts of single nucleotide polymorphisms in particular exons and introns of the human genome based on the data set of 1,222 individuals of Polish origin that comprises 41,836,187 polymorphisms. In particular, chromosomes 1 and 22 were considered as representatives of two markedly different DNA molecules, since HSA01 represents the longest and HSA22 is one of the shortest chromosomes. The results demonstrate that outer (first, last) exons as well as the first introns harbour significantly more SNPs than other genic regions. The observed differences in counts reflect the distinct functional roles of those genomic units.

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Section: Discussionmentioning

confidence: 99%

Exploring the Distribution of Single Nucleotide Polymorphisms Across Human Exons and Introns

Fraszczak,

Liu,

Mielczarek

et al. 2024

Preprint

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“…SNPs in intronic regions might cause diseases and alter the genotype-phenotype association by generating splice variants of transcripts and promoting or disrupting the binding and function of long noncoding RNAs (lncRNAs) (such as rs3731864 G/A and rs3731865 G/C). SNPs in the 5′-UTR regions can potentially affect translation, whereas those in the 3′-UTR region (i.e., rs17235416 + TGTG/−TGTG) impact the binding of microRNAs (miRNAs) 65,66 . Intronic sequences might be conserved, as they contain expression-regulating elements that impose functional constraints on their evolution 67,68 .…”

Section: Discussionmentioning

confidence: 99%

Association of SLC11A1 polymorphisms with anthropometric and biochemical parameters describing Type 2 Diabetes Mellitus

Kavian

Sargazi

Majidpour

et al. 2023

Sci Rep

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Diabetes, a leading cause of death globally, has different types, with Type 2 Diabetes Mellitus (T2DM) being the most prevalent one. It has been established that variations in the SLC11A1 gene impact risk of developing infectious, inflammatory, and endocrine disorders. This study is aimed to investigate the association between the SLC11A1 gene polymorphisms (rs3731864 G/A, rs3731865 C/G, and rs17235416 + TGTG/− TGTG) and anthropometric and biochemical parameters describing T2DM. Eight hundred participants (400 in each case and control group) were genotyped using the polymerase chain reaction-restriction fragment length polymorphism (PCR–RFLP) and amplification-refractory mutation system-PCR (ARMS-PCR) methods. Lipid profile, fasting blood sugar (FBS), hemoglobin A1c level, and anthropometric indices were also recorded for each subject. Findings revealed that SLC11A1–rs3731864 G/A, –rs17235416 (+ TGTG/− TGTG) were associated with T2DM susceptibility, providing protection against the disease. In contrast, SLC11A1–rs3731865 G/C conferred an increased risk of T2DM. We also noticed a significant association between SLC11A1–rs3731864 G/A and triglyceride levels in patients with T2DM. In silico evaluations demonstrated that the SLC11A2 and ATP7A proteins also interact directly with the SLC11A1 protein in Homo sapiens. In addition, allelic substitutions for both intronic variants disrupt or create binding sites for splicing factors and serve a functional effect. Overall, our findings highlighted the role of SLC11A1 gene variations might have positive (rs3731865 G/C) or negative (rs3731864 G/A and rs17235416 + TGTG/− TGTG) associations with a predisposition to T2DM.

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“…A recent study found that introns were involved in the gene splicing in eukaryotes, and that the mutation of introns might change the splicing efficiency, which resulted in the change of amino acid coding and eventually affected the biological traits [ 38 , 39 ]. Even if the intron mutation has no effect on the amino acid sequence, it may also result in the inactivation of the splicing site, or it may contain enhancer sequences to promote the specific transcription of the gene, affecting the animal phenotype [ 40 , 41 ]. The correlation between the SNPs on the introns and the milk fat traits of cattleyak may have a causal mutation, or it may be that these five SNPs are closely related to the SNPs on the exons.…”

Section: Discussionmentioning

confidence: 99%

Polymorphisms of SORBS1 Gene and Their Correlation with Milk Fat Traits of Cattleyak

Yang

Min

Zhu

et al. 2021

Animals

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This study aimed to find the SNPs in the SORBS1 gene of cattleyak, analyze the relationship between its polymorphisms and the milk fat traits, and find potential molecular markers for the milk fat traits of cattleyak. The polymorphism of the SORBS1 gene in 350 cattleyak from Hongyuan County (Sichuan, China) were detected by PCR and DNA sequencing, and the correlation between these SNPs and the milk production traits of cattleyak was analyzed. The results showed that there were nine SNPs in the CDS and their adjacent non-coding regions of the SORBS1 gene, and all SNPs have three genotypes. The correlation analysis found that the genotypes with superior milk fat traits in the other eight alleles were homozygous genotypes with a high genotype frequency except the g.96284 G > A (c.3090 G > A) (p < 0.05). However, at locus g.96284 G > A, the milk fat percentage, monounsaturated fatty acids (MUFAs), polyunsaturated fatty acids (PUFAs) and saturated fatty acids (SFAs) of the GA genotype were significantly higher than that of GG and AA genotypes (p < 0.05). Among these SNPs, three SNPs (g.6256 C > T (c.298 C > T), g.24791 A > G (c.706 A > G) and g.29121 A > G (c.979 A > G)) caused the amino acids change. The genotypes of the three SNPs consist of three haplotypes and four diplotypes. The amino acid mutation degree of diplotype H1–H1 (CCAAAA) was the highest, and its milk fat percentage, MUFAs, PUFAs and SFAs were also the highest (p < 0.05). Taken together, we found nine SNPs in the SORBS1 gene that are closely related to the milk fat traits of cattleyak. Moreover, the mutation of amino acids caused by SNPs had positive effects on the milk fat traits of cattleyak. H1-H1 is the dominant diplotype which significantly related to the milk fat traits of cattleyak. This study provides a new molecular marker and theoretical basis for screening the milk fat traits of cattleyak.

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Deciphering the association of intronic single nucleotide polymorphisms of crystallin gene family with congenital cataract

Cited by 18 publications

References 42 publications

Exploring the Distribution of Single Nucleotide Polymorphisms Across Human Exons and Introns

Exploring the Distribution of Single Nucleotide Polymorphisms Across Human Exons and Introns

Association of SLC11A1 polymorphisms with anthropometric and biochemical parameters describing Type 2 Diabetes Mellitus

Polymorphisms of SORBS1 Gene and Their Correlation with Milk Fat Traits of Cattleyak

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