Course No. 7 “Correlation of Disease Genes to Phenotypes”

 

Problem 1

This course focuses on the correlation of a disease gene to the phenotype. The following module demonstrates how NCBI resources such as literature, expression and structure information can help provide potential functional information for disease genes.

Mutations in the HFE gene are associated with the hemochromatosis disease. A laboratory working on the hemochromatosis disease wants to elucidate the biochemical and structural basis for the function of the mutant protein.

In this exercise, we have the following goals:

1. Determining what is known about the HFE gene and protein (using Entrez Gene).
2. Determining identified
SNPs and their locations in the HFE gene (using dbSNP).
3. Learning more about the hemochromatosis disease and its genetic testing (using
OMIM and Gene Tests)
4. Elucidating the biochemical and structural basis for the function of the wild type and the mutant protein, if possible.

Step 1. Determining what is known about the HFE gene and protein (using Entrez Gene):

Search for 'HFE" in Entrez Gene. One entry is for the human HFE gene. Retrieve the entry by clicking on the HFE link. List some of the HFE gene aliases. What is the name and function of the protein encoded by the HFE gene?

What is the location and orientation of the HFE gene on the human genome? List the genes adjacent to it.

How many alternatively spliced products have been annotated for the HFE gene when the RefSeq mRNA entries were reviewed? Which is the longest splice variant?

What are the phenotypes associated with the mutations in the HFE gene?

Step 2. Determining identified SNPs and their locations in the HFE gene:

From the Links menu on the top right hand side of the page, click on the "SNP:GeneView" to access a list of the known SNPs (reported in dbSNP).

By default, the SNPs in the coding region of a gene are reported. Additional SNPs, such as those located in an upstream region or the introns can be viewed by selecting the "in gene region" box and clicking Refresh. To view the SNPs associated with phenotypes, select the “Clinical Source” box and click Refresh. We will concentrate on the cys282tyr mutant in the following analysis.

Step 3. Learning more about the hemochromatosis disease and its genetic testing:

Click on the OMIM link next to the one of the SNPs in the Clinically Associated column. Click on the link to the HFE gene (61309).  What are the clinical features of hemochromatosis? List the 5 types of iron-overload disorders labeled hemochromatosis. Which of these is associated with mutations in the HFE gene?  Open the Table of Contents menu by clicking on it.

How many allelic variants of the HFE gene have been reported? What is the phenotype associated with the Cys282Tyr mutant?

Go back to the previous HFE page in the OMIM database.  Click on the Clinical Resources link under the External Links menu.  Click on the Gene Tests link. Click on the HFE associated hemochromatosis link and then on the GeneReviews link. Mutation analysis is available for which of the HFE alleles?

List one explanation for the hemochromatosis phenotype caused by the Cys282Tyr mutant.

Step 4. Elucidating the biochemical and structural basis for the function of the wild type and mutant proteins, if possible:

Visualization of cysteine 282 on the structure of the hemochromatosis protein:

Go back to the Entrez Gene report. In the section "Genomic Region, Transcripts and products", click on the protein accession number NP_000401. Click on the protein 3D structure link and then on the 2nd structure Hfe (Human) Hemochromatosis Protein link. Note the structure contains two proteins, hemochromatosis and beta 2 microglobulin.  Click on the View structure link. In the structure window, select Style—Edit global style and check on the box for Virtual disulphides and then on the Done button. In the sequence window, View—Find pattern and type tcqv and click on OK.  Highlight only the c residue.  It forms one of the disulphide bridges. 

You can now easily explain why the C282Y mutant has an altered function.

The interaction of hemochromatosis protein with beta-2-microglobulin allows cell surface presentation of the complex. Once on cell surface, the hemochromatosis protein regulates iron absorption by regulating the interaction of transferrin receptor with transferrin. However, the Cys282Tyr mutant does not interact with beta-2-microglobulin and thus fails to regulate the interaction of transferrin receptor with transferrin leading to iron overload. Cysteine 282 is involved in formation of a disulphide bridge. Its mutation to tyrosine will alter the folding of the protein.

 

Questions, Comments:  Medha Bhagwat, PhD