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Related Concept Videos

Genetic Variation01:25

Genetic Variation

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Genetic variation is the diversity in DNA sequences found among individuals of the same species. This diversity is crucial for a species' survival because it helps organisms adapt to environmental changes. Genetic variation begins with fertilization, where an egg and sperm cell merge. Each of these cells carries 23 chromosomes, up to 46 in the fertilized egg. Chromosomes are long DNA strands that contain genes, the basic units of heredity.
Genes exist in different versions called alleles,...
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Comparing Copy Number Variations and SNPs02:26

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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.
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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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Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
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Related Experiment Video

Updated: Jul 11, 2025

Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay EMSA and DNA-affinity Precipitation Assay DAPA
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Matching variants for functional characterization of genetic variants.

Sebiha Cevik1, Pei Zhao2,3, Atiyye Zorluer1

  • 1Rare Disease Laboratory, School of Life and Natural Sciences, Abdullah Gul University, Kayseri 38080, Turkey.

G3 (Bethesda, Md.)
|November 7, 2023
PubMed
Summary

This study used Caenorhabditis elegans to analyze variants in the IFT-140 gene, identifying two specific mutations (P702A and W937stop) that cause ciliary defects, aiding in the interpretation of human genetic diseases.

Keywords:
IFT140Mainzer–Saldino syndromeciliaciliopathymatching variants

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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
  • Cell Biology
  • Developmental Biology

Background:

  • Genetic diagnosis advances rapidly, yet interpreting genetic variants, especially missense mutations, remains challenging.
  • Computational predictions and high-throughput experiments have limitations in variant interpretation.
  • Utilizing model organisms and existing mutant resources can aid in understanding gene function and variant effects.

Purpose of the Study:

  • To functionally characterize missense and stop-codon variants in the intraflagellar transport protein 140 (IFT-140) gene.
  • To use Caenorhabditis elegans as a model to assess the phenotypic impact of IFT-140 variants, including those matching human disease variants.
  • To provide experimental support for the interpretation of human genetic variants associated with ciliopathies.

Main Methods:

  • Generated and analyzed ten variants (eight missense, two stop codons) in the C. elegans IFT-140 gene.
  • Created specific human-matching variants (MatchVars) using CRISPR/Cas9 gene editing in C. elegans.
  • Assessed ciliary phenotypes, including cilia length, intraflagellar transport (IFT) accumulation, and protein localization.

Main Results:

  • Two variants, IFT-140(P702A) and IFT-140(W937stop), phenocopied the null mutant phenotype, exhibiting short cilia, IFT accumulations, and protein mislocalization.
  • Other analyzed variants did not show significant ciliary defects in C. elegans.
  • The study successfully generated and functionally validated C. elegans MatchVars for human IFT-140 variants.

Conclusions:

  • The C. elegans model is effective for the functional assessment of IFT-140 variants.
  • The identified phenotypic variants (P702A and W937stop) provide valuable insights into IFT-140 function and human disease mechanisms.
  • This approach using model organism mutants aids in the interpretation of genetic variants of unknown significance in human diseases.