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I think it is because the question stem asks about the deficiency that "DIRECTLY" affects a process. Vitamin D directly affects calcium reabsorption whereas it is the rise in Calcium (caused by Vitamin D) that then negatively regulates PTH production (so Vitamin D indirectly regulates PTH). The "directly" wording has gotten the best of me more than a few times so now I've become hyper-aware of that wording.
Also, I just realized it asks about "vitamin deficiency" and calcium is technically a mineral :/
Adding on, hoarseness + difficulty swallowing means something is pushing on the recurrent laryngeal.
Murmur in the second right intercostal space = AR, AS, or Pulm regurg --> AR associated with thoracic aortic aneurysm, or at minimum, you can infer it's a cardiac etiology
The dyspnea, dysphagia, stridor, and cough are pretty indicative of a mediastinal mass. So expansion of the aorta can cause compression of the esophagus, trachea, recurrent laryngeal nerve, etc. depending on the severity of it.