Sarcoidosis: This condition is characterized by the formation of granulomas in various parts of the body, including the lungs, skin, and bones. It can lead to low lymphocyte counts due to lymphocyte sequestration in granulomas, low vitamin D levels due to granulomatous inflammation affecting vitamin D metabolism, and bone nodules as part of the disease's skeletal manifestations.

Lymphoma: Certain types of lymphoma can cause low lymphocyte counts, and some patients may have low vitamin D levels due to various factors, including decreased sun exposure or malabsorption. Bone nodules could be part of the lymphoma's bone marrow involvement.
Chronic Kidney Disease (CKD): CKD can lead to low vitamin D levels due to impaired vitamin D activation in the kidneys. Low lymphocyte counts can occur in advanced CKD due to uremia. Bone nodules might be seen in the context of renal osteodystrophy, which includes a range of bone abnormalities associated with CKD.
HIV/AIDS: This condition can cause a significant decrease in lymphocyte counts, particularly CD4+ T cells. Low vitamin D levels are common in HIV-infected individuals, and bone nodules could be related to opportunistic infections or malignancies affecting the bone.

Multiple Myeloma: Although less common, multiple myeloma is a critical diagnosis not to miss. It can cause low lymphocyte counts, low vitamin D levels (due to impaired renal function or direct effects on bone), and bone nodules (as part of the disease's bone marrow infiltration and lytic lesions).
Tuberculosis (TB): TB can lead to low lymphocyte counts, especially in advanced disease, and low vitamin D levels have been associated with TB, possibly due to the disease's impact on vitamin D metabolism. Bone nodules could be part of skeletal TB.

Langerhans Cell Histiocytosis (LCH): This rare disorder can cause low lymphocyte counts, low vitamin D levels, and bone nodules. LCH leads to an accumulation of Langerhans cells in various organs, including the bone, where it can cause lytic lesions and nodules.
Gastric Bypass-associated Conditions: Rarely, individuals who have undergone gastric bypass surgery might develop low vitamin D levels due to malabsorption. If such a condition leads to significant immunocompromise or is associated with another underlying disease, it could potentially result in low lymphocyte counts and bone nodules, although this would be an uncommon presentation.