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Related Concept Videos

Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

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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-GWAS01:11

Genome-wide Association Studies-GWAS

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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.
GWAS does not require the identification of the target gene involved in...
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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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Pleiotropy01:33

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Pleiotropy is the phenomenon in which a single gene impacts multiple, seemingly unrelated phenotypic traits. For example, defects in the SOX10 gene cause Waardenburg Syndrome Type 4, or WS4, which can cause defects in pigmentation, hearing impairments, and an absence of intestinal contractions necessary for elimination. This diversity of phenotypes results from the expression pattern of SOX10 in early embryonic and fetal development. SOX10 is found in neural crest cells that form melanocytes,...
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Principles of Pharmacogenetics: Types of Genetic Variants01:27

Principles of Pharmacogenetics: Types of Genetic Variants

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The human genome is over 99.9% identical between individuals, yet genetic differences exist at millions of bases. The human genome contains approximately 3 million variant positions per individual, many of which are heterozygous, contributing to genetic diversity and individual traits. Genetic variations include single-nucleotide polymorphisms (SNPs), insertions, deletions, and copy number variations (CNVs).SNPs, the most common variation, involve single-base changes in DNA. These can be...
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Related Experiment Video

Updated: Apr 1, 2026

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
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A non-synonymous single-nucleotide polymorphism associated with multiple sclerosis risk affects the EVI5 interactome.

Alessandro Didonna1, Noriko Isobe2, Stacy J Caillier2

  • 1Department of Neurology, alessandro.didonna@ucsf.edu.

Human Molecular Genetics
|October 5, 2015
PubMed
Summary

Researchers identified EVI5 as a key gene for multiple sclerosis (MS) risk. A specific genetic variant alters EVI5 protein interactions, revealing new links to lipid metabolism and MS pathogenesis.

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Area of Science:

  • Genetics
  • Immunology
  • Neuroscience

Background:

  • Genetic loci for multiple sclerosis (MS) risk are known, but distinguishing causative variants from linked single-nucleotide polymorphisms (SNPs) is challenging due to genome-wide linkage disequilibrium.
  • The 1p22.1 locus is associated with MS risk, but the specific gene and variants conferring risk remain unclear.

Purpose of the Study:

  • To identify the most plausible disease risk gene within the 1p22.1 locus associated with multiple sclerosis (MS).
  • To investigate how a risk-associated SNP affects the function and interactions of the identified gene.
  • To uncover novel molecular mechanisms and therapeutic targets for MS by analyzing the altered interactome.

Main Methods:

  • Fine mapping and meta-analysis to pinpoint the disease risk gene at the 1p22.1 locus.
  • Analysis of exonic SNPs to determine their impact on protein structure and function.
  • Immunoprecipitation followed by mass spectrometry to identify protein interactors of wild-type and mutated EVI5.
  • Functional enrichment analysis of identified interactors, focusing on lipid metabolism pathways.

Main Results:

  • EVI5 was identified as the most likely MS risk gene in the 1p22.1 locus.
  • A risk-associated SNP alters the superficial hydrophobicity of the EVI5 coiled-coil domain, affecting its interactome.
  • Novel disease-specific interactors were identified, functionally linked to lipid metabolism.
  • A new interaction between the risk variant of EVI5 and sphingosine 1-phosphate lyase (SGPL1) was discovered.

Conclusions:

  • EVI5 is a critical MS risk gene, and its function is modulated by specific genetic variants.
  • The risk variant of EVI5 influences MS pathogenesis through altered interactions with proteins involved in lipid metabolism, notably SGPL1.
  • This finding provides new insights into MS pathology and suggests SGPL1 as a potential therapeutic target for managing MS.