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Related Concept Videos

Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

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Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
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Single Nucleotide Polymorphisms-SNPs01:05

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A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
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Exon Recombination02:32

Exon Recombination

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The evolution of new genes is critical for speciation. Exon recombination, also known as exon shuffling or domain shuffling, is an important means of new gene formation. It is observed across vertebrates, invertebrates, and in some plants such as potatoes and sunflowers. During exon recombination, exons from the same or different genes recombine and produce new exon-intron combinations, which might evolve into new genes. 
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RNA Splicing01:32

RNA Splicing

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Splicing is the process by which eukaryotic RNA is edited before its translation into protein. The RNA strand transcribed from eukaryotic DNA is called the primary transcript. The primary transcripts that become mRNAs are called precursor messenger RNAs (pre-mRNAs). Eukaryotic pre-mRNA contains alternating sequences of exons and introns. Exons are nucleotide sequences that code for proteins, whereas introns are the non-coding regions. In RNA splicing, introns are removed and exons are bonded...
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Alternative RNA Splicing02:18

Alternative RNA Splicing

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Alternative RNA splicing is the regulated splicing of exons and introns to produce different mature mRNAs from a single pre-mRNA. Unlike in constitutive splicing where a single gene produces a single type of mRNA, alternative splicing allows an organism to produce multiple proteins from a single gene and plays an important role in protein diversity.
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Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
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A common intronic single nucleotide variant modifies PKD1 expression level.

Zhengmao Zhang1, Jon Blumenfeld2,3, Andrew Ramnauth1

  • 1Departments of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, USA.

Clinical Genetics
|August 27, 2022
PubMed
Summary
This summary is machine-generated.

A novel genetic variant, rs3874648G>A, in the PKD1 gene modifies autosomal dominant polycystic kidney disease (ADPKD) expression by affecting splicing. This finding helps explain ADPKD

Keywords:
ADPKDhypomorphic variantintronnext-generation sequencingsingle nucleotide variant

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Determining the Likelihood of Variant Pathogenicity Using Amino Acid-level Signal-to-Noise Analysis of Genetic Variation
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Area of Science:

  • Genetics and Genomics
  • Molecular Biology
  • Population Genetics

Background:

  • Autosomal dominant polycystic kidney disease (ADPKD) exhibits unexplained phenotypic variability, potentially due to unidentified genetic factors.
  • Approximately 10% of ADPKD cases lack detectable causal mutations, suggesting the involvement of unrecognized risk variants in PKD1 and PKD2 (PKD1/2).

Purpose of the Study:

  • To identify risk variants within PKD genes using population genetic analyses.
  • To investigate the functional impact of identified variants on PKD1 expression and ADPKD pathogenesis.

Main Methods:

  • Population genetic analysis using Wright's F-statistics (Fst) on single nucleotide variants (SNVs) in PKD1 from the 1000 Genomes Project (1KG).
  • Genotyping of 388 subjects from the Rogosin Institute ADPKD Data Repository.
  • In silico and molecular genetics analyses of variants exceeding the 90th percentile Fst score, including RT-PCR and splicing assays.

Main Results:

  • Identified a deep intronic SNV, rs3874648G>A, in PKD1 intron 30, located within a conserved Tra2-β splicing regulator binding site.
  • Demonstrated that the rs3874648-A allele increases Tra2-β binding, activates a cryptic splice site, and leads to a premature stop codon, reducing full-length PKD1 transcript levels.
  • Observed lower PKD1 transcript levels in peripheral blood leukocytes (PBL) of rs3874648-G/A carriers compared to homozygotes.

Conclusions:

  • The rs3874648G>A variant acts as a PKD1 expression modifier, attenuating gene expression via the splicing regulator Tra2-β.
  • The ancestral G allele appears to maintain PKD1 expression and is predominant across populations.
  • This study identifies a novel mechanism contributing to ADPKD phenotypic variability and provides a potential explanation for cases with undetectable mutations.