Problem
Background information for reference:
Imagine that you are a geneticist at a hospital, and you are given a file for a patient who has the following history.
The patient, Jane Doe, is 30 years old. Her second pregnancy had to be terminated because the baby she was carrying had abdominal wall defects (exomphalos) as well as enlarged organs inside the abdomen (visceromegaly). In contrast, her first pregnancy was normal, and the baby was born without any complications. Her husband's family has no history of the condition and neither does her own family.
To gain insight into what the cause of the malformed baby could be, you order whole exome sequencing of the patient's DNA. You get back the results and find out that Jane is heterozygous at four loci (candidate genes 1-4); each with SNPs that are not common in the general population. Their sequences are found in the appendix. Your goal as a geneticist is to determine which gene has the causative mutation that led to her baby having the malformations and advise Jane about her options.
Task
1. Conduct a BLAST search using the candidate gene sequences. What are the identities of each of the candidate genes? What do they encode?
2. What kind of changes are present in the sequences of each of the candidate genes? What is the consequence of each mutation?
3. Is the mutation in the protein coding region of the gene? If it is, how would you experimentally determine that this is the protein coding region?
4. Based your conclusions, which one is the most likely to be the causative mutation that led to the fetal malformations? Explain your reasoning and make a convincing case.
5. Is there a disorder or syndrome associated with the gene you chose in 4? If there is, what is it?