Rare diseases · Sign or symptom
Kidney stone
HP:0000787
What it means
Kidney stones (calculi) are mineral concretions in the renal calyces and pelvis that are found free or attached to the renal papillae.
Nephrolithiasis is derived from the Greek words nephros (kidney) and lithos (stone) and the suffix iasis (process) and refers to the condition of having one or more kidney stones. In practice, nephrolithiasis is used interchangably. In contrast to nephrolithiasis, diffuse renal parenchymal calcification is called nephrocalcinosis. Stones that develop in the urinary tract (known as nephrolithiasis or urolithiasis) form when the urine becomes excessively supersaturated with respect to a mineral, leading to crystal formation, growth, aggregation and retention within the kidneys. Crystals or foreign bodies can act as a nidus for further stone formation. The resulting kidney stones (calculi) lead to symptoms if they become impacted in the ureter.
In everyday care
Most people with this sign do not have a rare disease — it appears in common conditions far more often. These general reference pages cover the same topic:
Rare diseases that can present with this60
Very common80–99%
10- 2p21microdeletion syndrome
- Cystinuria
- Dent disease
- Hypotonia-cystinuria syndrome
- Leukomelanoderma-infantilism-intellectual disability-hypodontia-hypotrichosis syndrome
- Leukonychia totalis
- Medullary sponge kidney
- Primary hyperoxaluria type 1
- Primary hyperoxaluria type 2
- Primary hypomagnesemia with hypercalciuria and nephrocalcinosis with severe ocular involvement
Common30–79%
12- Adenine phosphoribosyltransferase deficiency
- Alkaptonuria
- Congenital primary megaureter
- Cushing syndrome due to bilateral macronodular adrenocortical disease
- Cystinosis
- Distal renal tubular acidosis
- FLOTCH syndrome
- Hereditary hypophosphatemic rickets with hypercalciuria
- Hyperparathyroidism-jaw tumor syndrome
- Hypocalcemic vitamin D-resistant rickets
- Microcephaly-facial dysmorphism-ocular anomalies-multiple congenital anomalies syndrome
- Parathyroid carcinoma
The range is how often this sign appears among people diagnosed with each disease — it is not a probability of having any of them. Many of these signs also occur in common, non-rare conditions. A sign on this page is a conversation to have with a clinician, not a conclusion.
Part of the broader category
Also called: Kidney stones · Nephrolithiasis · Renal calculi · Renal stones
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Start free with EleplanThis page uses the Human Phenotype Ontology (2026-06-23) — Human Phenotype Ontology Consortium, hpo.jax.org. Disease associations from Orphanet (INSERM), CC BY 4.0. Content is educational and is not medical advice.