Twins' Case Study

Welcome to your Patients!

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.   

For a quick view of information on the twins’ case, you are welcome to read a fictitious referral for genetic screening here: https://bit.ly/Oct21_DemoCaseReferral

Researching the Referral

Find Information about this DISORDER from Human-Curated sources:

1. Search NCBI’s MedGen database with:  dystonia AND spasticity AND hyperactivity AND sleep disturbance

What is a possible diagnosis for the twins?

2. There are many relevant publications on and linked from the MedGen record. Where can you find them?  Write down any PMIDs that are of interest to you.

• • • PubMed Clinical Queries – quick ways to pull up categories of recent publications.
    • ClinicalTrials.gov – to see if any are currently enrolling participants.
    • Consumer Resources – to provide as an additional resource for the family.
      
      

3. Let’s learn more about this disorder and work on a Differential Diagnosis.

Which other disorders could have been considered and which genes are associated with each?  (Hint: Check the GeneReviews>Differential Diagnosis link.)

THE LAB RESULTS CAME BACK:  https://bit.ly/Oct21_DemoCaseLabResults

Does the lab results support the preliminary diagnosis?

1. Let's map these results onto a diagram of some relevant metabolic pathways....
   How do the results map to the biological pathways related to l-Dopa?  (which seemed to work for a while)

Based on your research and the results of the Lab Test, what do you think is wrong with Alexis & Noah?

Finding a Genetic Test and Learning from the Genetic Test Results

4. From the MedGen record, in the Genetic Testing Registry section on the right – click (See all) and then use the filters on the left to narrow down the list to find a genetic test that you could order for them.

(For this case-study, this should be a CLIA-certified clinical lab in California.)  Write down the GTR Test ID.

THE GENETIC TEST RESULTS ARE IN:  https://bit.ly/Oct21_DemoCaseGeneticResults 

Remember that metabolic pathway that we looked at above? 
How do these genetic test results relate to what the lab test results found?   
(Go back and map the Genetic Test results with the Lab Results in the image.)

What does the genetic testing laboratory say about the twins' diagnoses in the report?

Understanding and Validating the Genetic Test Results

5. To validate what is asserted by this clinical testing laboratory, check the ClinVar database.

Scroll down to the Submitted interpretations and evidence section and look at what the various laboratories assert about the pathogenicity of each variation.  what do you conclude about the validity of the genetic testing laboratory’s calls for each variant?

In preparation for the next step, 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.).

Molecular Biology Research – Normal gene function and expression

Information about this gene from Human-Curated sources:

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

7. From the Gene record, scroll down to the General gene information>Gene Ontology section to learn more about the protein produced from this gene. This section displays 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).    (terms assigned by the Gene Ontology Consortia’s Curators)

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

Does this make sense based on the summary of the Gene that you just found? 

What specific function(s) does this protein have?

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

8. Scroll down to the “Expression” section to see in which tissues this gene is expressed and, since the protein is maintained within the cell, where it functions.

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

 Do any of these correlate with some of the twins’ symptoms?

Based on your understanding of the complexity of gene expression, how might you explain some of the differences in symptoms observed in the twins?  (This is a thought question, there isn’t a specific answer.)

Molecular Biology Research – Variant location and potential impact

Information about this gene determined from sequence-based sources:

9. On the right-hand side of the Gene record, click the “RefSeqGene” link to see the “Graphic” view of the gene structure defined on the chromosome on a RefSeqGene nucleotide page.

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

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.

 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?

11. From either the Gene or Protein record, can click a link to 3D Structure to visualize experimentally-determined molecular structures for this protein. In the 3D structure you can see precisely the locations of the amino acids affected by the genetic variations.

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. Completing the cycle, go back to the Gene record and scroll down to the Pathways from PubChem section - in which Metabolic Pathways does this protein participate? Does the role of this enzyme in important pathways validate the diagnostic and therapeutic choices (so far…. l-DOPA)?

WHAT IS WRONG WITH ALEXIS & NOAH?

HOW CAN IT BE FIXED?