What part of kidney involved in converting/metabolizing vit d?can that part be permanently damaged by bacteria and/or congenital defect ?

See answer: Metabolism of vit d (d2 and d3) from the skin and intestine into its biologically and hormonally-active form known as 1, 25-dihydroxycholecalciferol (calcitriol) involves the parathyroid gland, liver, and the enzyme vd3 1a hydroxylase located in the proximal tubule of the kidney. There is a rare congenital deficiency of this enzyme but deficiency usually due to severe chronic kidney disease/failure.

Kidney: It can be damaged when the bacteria damages the whole kidney.( does not do specific to that area). Same thing goes to congenital defects.

Proximal convoluted : Tubule. There are vitamin d3 receptors in the kidney to do the conversion to the active form. You can always support it via nutitioinal supplementation or rx dose. So talk with your nephrologist, as this is very important for your child. If your child still has 2 kidneys, even with congenital defect, supplementation will be helpful, as just about all organs depend on that important hormone/vitami.

See below: The final step of vitamin d activation ( 1-hydroxylation ) occurs in renal tubular cells. Recurrent pyelonephritis and congenital defects leading to obstructive uropathy ultimately result in damaging renal tubular cells.