The Twins' Case Study

Welcome to your Patients!

Alexis & Noah, 12 year old twins have been brought to you for a second (well, third) opinion... Diagnosis:         Originally Cerebral Palsy, then Sagawa Dystonia, and then.... Key Symptoms: Dystonia with muscle spasticity, also severe sleep disturbance and hyperactivity. Family history: “Unremarkable”, with several members of the family diagnosed with Major Depressive Disorder and mother diagnosed with Fibromyalgia. The fraternal twins exhibited seemingly classic cerebral palsy symptoms from shortly after birth. An MRI of Noah’s brain provided supporting evidence. After five years, the twins seemed to be getting worse – particularly later in the day. After the mother read a 1991 LA Times article about a “treatable cerebral palsy-like syndrome” (Sagawa Dystonia), they met with the treating physician and were given a test dosage of L-Dopa with immediate, positive results. However, sleep disturbances and hyperactivity levels continued and at 12 years of age, Alexis’s severe untreatable respiratory problems prompted a reassessment of their diagnosis.

Researching the Referral

1. To learn more about the proposed diagnosis, search MedGen (https://www.ncbi.nlm.nih.gov/medgen/) with: 

If you need it, you can click here to get to a link for the Medgen record page.

Try This!

Based on the results of that search, what is a possible diagnosis for the twins and how does this correspond to the preliminary diagnosis listed in the referral?

Which features within this summary seem to confirm that this is a possible disorder to be considered for the diagnosis?

Note:  GeneReviews® is a project run by the University of Washington - producing expert-authored, point-of-care information with clinically relevant and medically actionable information for inherited conditions.  It is an incredible review article-type of resource, and is thus featured in it's own section on relevant MedGen records - as an abstract with links to key sections.  You should consider accessing and reading the whole article!

Which other conditions you should consider during your work-up? 

 

Which other conditions and their corresponding genes you should consider during your work-up?  

What genes do you think you might target to identify if the twins have any variants associated with with this diagnosis?

Which laboratory test(s) could you order?  (Hint: Check what it says about CSF neurotransmitters and pterins.)

Which analytes are "flagged" as outside normal ranges?

How does the information in the lab test correspond to the preliminary diagnosis?  Does this support it?

 For this disorder, is a genetic test(s) recommended for validation? 



 

What should you take into consideration before ordering a Genetic Test?

• • • Pros
      • Genetic tests are decreasing in cost & are not particularly invasive.
      • A well-known genetic lesion can sometimes help in diagnosis and/or drug/therapy selection - may provide actionable information.
      • A finding may predict disorders before symptoms begin for proactive & preventative care.
    • Cons
      • We are early in our understanding of genes, gene variants and disease:  Failure to detect a pathogenic variant does not rule out the diagnosis.
      • Prediction isn’t guaranteed - as pathogenic variants sometimes do not have consistent phenotypic impact in all patients (penetrance, severity, multi-genic & environmental influences).
      • Lack of coverage by some insurance companies…

You discuss the diagnosis and mention the availability of a genetic test to help clarify and validate the twins' issues The family recently moved to San Diego where Joe became the CIO of a biotechnology company which supports human genome research and Retta has become a strident patient advocate. Thus, they are familiar with the latest technologies and are very interested in participating in cutting-edge research studies that may have an impact and help other patients as well. They are eager to try genetic testing to see if ths can help clarify what is happening in the twins down to the molecular level.

Finding a Genetic Test and Understanding the Results

1. 1. From the MedGen record, in the Genetic Testing Registry section on the right – click (See all) to retrieve a list of relevant tests.

Write down the GTR Test ID.

What are the specific gene and variations identified in the twins?  (Read the test results, sometimes it is really helpful!)

What does the genetic testing laboratory say about the twins' diagnoses in the report?  Based on the information in the GeneReviews article, does this make sense?

Validating the Genetic Test Results and Learning More About the Variant(s)

5. To validate what is asserted by this clinical testing laboratory, search NCBI’s ClinVar database  (https://www.ncbi.nlm.nih.gov/clinvar/) with:   

What does ClinVar say in the “Interpretation” field about each genetic variation?



In preparation for the next step of this case study (learning about the biology), find and write down the HGVS description for each variant. This will help to find the location of each of the variants later, especially in the gene (NG_  g.) & the protein (NP_  p.).

what do you conclude about the validity of the genetic testing laboratory’s calls for each variant?

Remember that metabolic pathway that we looked at (above)? How do the genetic test results relate to what the lab test results implied?

Finding Patient Education Materials to Share

1. To assist you further in learning about this disorder and for preparation for discussions with your patient, there are additional MedGen links to:

• • • PubMed – retrieves all relevant publications about this disorder.
    • PubMed Clinical Queries – quick ways to pull up categories of recent publications.
    • ClinicalTrials.gov – to see if any are currently enrolling participants.

You discuss the new diagnosis and hand the twins’ parents, Retta & Joe, some Patient Education materials. Retta would like to know why L-Dopa seemed to work initially and understand why you are recommending altering the treatment based on the precise molecular information you were able to obtain for the twins.

Learning About the Implicated Gene

6. On the MedGen or ClinVar record, click the link for the Gene Symbol identified as having variants in the twins.

If you need it, you can click here to get to a link for the Medgen record page.

Try this!

Or click here to get a link to go straight to the Gene record page.

Try this!

Read the Summary section and identify what does this gene normally does.

Here's some additional information which may also help you - I've pulled it together from an old molecular biology textbook available on the NCBI Bookshelf!

FULLY ANNOTATED PATHWAY

8. The Gene Ontology (GO) Consortium's mission is to build a comprehensive, human-readable and computable, hierarchical knowledgebase for the molecular functions, cellular locations, and processes that gene products (usually proteins) carry out.

In the Gene record's “Gene Ontology” section, learn more about the gene's product (protein) with GO-assigned standardized terms for where this gene product is likely to be found within a cell (Component), what processes it is often involved in (Process), and what it does (Function).   

What type(s) of process(es) is/are this protein normally involved with?

What specific function(s) does this protein have?

In which component(s) (sub-cellular location) is this protein normally found?

Does this make sense based on the Gene Summary of the Gene that you found above? 

9. Scroll down to the Gene record's “Expression” section to see in which tissues this gene has been observed to be expressed.

In which tissues has this gene been found to be expressed?

Do any of these tissues correlate with those associated with the twins' symptoms?

 

  

Mapping and Understanding the Impact of the Variant(s)

So, you now know information about what the "wild-type" or non-variant-containing gene product does and where.  How might your patient's variant impact ths gene and it's product?  First, it depends upon where the variant is located and then it depends upon it's impact in that location.

Click here to see a graphic that I made based on the central dogma of molecular biology and how to systematically step through an assessment of variant location and possible physiological impact.

A Review of the Central Dogma of Molecular Biology & How to Assess and Predict Variant Impact

1. Genome/Chromosome:  First, let's map where that particular gene is within the chromosome.

How many transcript variants and encoded proteins are known to be produced by this gene? 

Where is/are the twins’ genetic variants located in this gene and in the mRNA?

Based on the position(s) of the variant(s) in the gene, what is the most likely mechanism for impacting the final gene product?  
(alter gene expression, influence transcript processing, or change encoded protein sequence)

10. On the right-hand side of the RefSeqGene page, can click the “Protein” link or go back to the Gene record and click the “RefSeq Proteins” link. Click “Graphics” to see a graphical view of the annotated regions curated on the protein sequence. The information shown in in these “tracks” of this view can help you to learn more about this protein.

Where in the protein sequence is/are the twins’ genetic variants located?

Take a look at the annotations shown in the Graphic view.  Based on where it the variant(s) is/are located, which might the variant(s) alter:

• the protein’s location (signal peptide)
• post-translational processing of the protein (cleavage site)
• post-translational modification of the protein (phosphorylation or methylation site, for example)
• the functional activity of the protein (domain, motif, and/or specific site/“key” residue – binding, active site, catalysis, for example)
• to learn more about the main functional regions of the protein click “Identify Conserved Domains”.

What might be the impact of the genetic variations on the protein’s function?

To make things easier for you right now….here’s a picture of the 3D crystal structure monomer of the Human SPR protein complex (PDB accession: 4Z3K) as displayed in

What do you think the change in amino acids might do to the 3D structure and function of the protein?
(I’ve given you some information in the box below….)

12. Now, to understand the role of the SPR protein in physiology, go back to the Gene record and scroll down to the Pathways from PubChem section - in which Metabolic Pathways does this protein participate?

What is wrong with your patient(s)?

Well what do you think?

The twins' parents ask:

• "What is wrong with them?"
• "Are we sure this is the right diagnosis this time?"
• "What do we do now?"

Take-away message!

Answer: