Notes on Lactose Intolerance and SNPs

Lactose Intolerance and SNPs

Amy's Test Results

• Amy's test results indicate she has an adult-onset lactose intolerance variant.
• This variant is located upstream of the lactase encoding LCT gene.

Location of the SNP

• The specific SNP is located 13,910 base pairs upstream of the translational start site of the LCT gene.
• This region functions as an enhancer.
• Enhancers contain binding sites for various transcription factors.
• These transcription factors increase the expression of the associated gene (LCT in this case).

The Role of Oct-1 Transcription Factor

• The SNP is located within the binding site for the Oct-1 transcription factor.
• The SNP can be either a cytosine (C) or a thymine (T).

Impact of Thymine (T) Variant

• If a thymine (T) is present at the SNP location:
  • It creates a higher affinity binding site for Oct-1.
  • This promotes LCT gene expression.
  • The LCT gene remains active into adulthood.

Impact of Cytosine (C) Variant (Amy's Case)

• Amy has the cytosine (C) variant at this position.
  • It leads to lower affinity binding of Oct-1.
  • Results in adult-onset lactose intolerance.

Phenotypic Consequences of a Single Base Pair Change

• This example shows how a single base pair change (SNP) in the genome can have phenotypic consequences for an individual.
• In this case, the SNP leads to a regulatory change affecting transcription levels.

Other Potential Impacts of SNPs

• SNPs can also lead to changes in:
  • RNA processing
  • RNA stability
  • Protein stability
  • Protein modification
  • Protein function
• These changes can affect other crucial biological processes.