IgA Nephropathy: This condition is characterized by mesangial hypercellularity and can sometimes present with tubular changes, including calcification, especially in more advanced or severe cases. The absence of immunofluorescence (IF) findings does not rule out IgA nephropathy, as the diagnosis is primarily based on the presence of IgA deposits, which might be missed if the biopsy sample is small or if the IF study is not adequately performed.

Focal Segmental Glomerulosclerosis (FSGS): While FSGS primarily affects the glomeruli, secondary changes in the tubules, including calcification, can occur, especially in advanced disease. Mesangial hypercellularity can also be seen in some forms of FSGS.
Alport Syndrome: This genetic disorder can lead to chronic kidney disease and may show a variety of glomerular and tubular changes, including calcification. However, Alport syndrome typically has a strong family history and specific ultrastructural changes in the glomerular basement membrane.
Lupus Nephritis: Although the IF is reported as negative, lupus nephritis can have a wide range of presentations, including mesangial hypercellularity and tubular damage. Lupus nephritis is known for its immune complex deposition, which might not always be detected.

Diabetic Nephropathy: Given the high prevalence of diabetes and its potential to cause renal disease, diabetic nephropathy should always be considered, even in the absence of typical glomerular changes like Kimmelstiel-Wilson lesions. Tubular calcification can occur in diabetic nephropathy.
Vasculitis (e.g., ANCA-associated vasculitis): While vasculitis might not directly cause tubular epithelial calcification, it can lead to a wide range of renal injuries, including glomerulonephritis with mesangial hypercellularity. Missing a diagnosis of vasculitis could have significant implications for patient management and outcome.

Cystinosis: A rare genetic disorder that leads to cystine accumulation within cells, causing damage to various organs, including the kidneys. It can result in renal failure and might show tubular calcification.
Primary Hyperoxaluria: A genetic disorder leading to excessive oxalate production, which can cause nephrocalcinosis and renal failure. The presence of tubular calcification could suggest this diagnosis, although it is rare.
Nephrocalcinosis due to other metabolic disorders: Disorders like distal renal tubular acidosis or hyperparathyroidism can lead to nephrocalcinosis, which might present with tubular epithelial calcification. These conditions are less common but should be considered based on clinical context and additional diagnostic findings.