Human Phenotype Ontology

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Examples Gene: MT-ND1, POLG, Region: M:1-1000 Variant: m.8993T>G, 1:g.10042757T>C rs3888511 MSCV_0000006, ClinVar: RCV000000015, Disease: Leigh syndrome, Phenotype: Retinopathy

Grandparent Node:
Abnormal renal morphology (HP:0012210)

Parent Node:
Nephrolithiasis (HP:0000787)

..Starting node
..Calcium nephrolithiasis (HP:0004724)

Term ID:

4724

Name:

Calcium nephrolithiasis

Synonym:

Ca kidney stone; Ca nephrolithiasis; Ca2+ kidney stone; Ca2+ nephrolithiasis; Calcium kidney stone

Definition:

The presence of calcium-containing calculi (stones) in the kidneys.

Comments:

Reference:

HP:0004724

Genes and Diseases:

Child Nodes:

........

Calcium oxalate nephrolithiasis (HP:0008672)

........

Calcium phosphate nephrolithiasis (HP:0012580)

Sister Nodes:

Struvite nephrolithiasis (HP:0030035)

Uric acid nephrolithiasis (HP:0000791)

Xanthine nephrolithiasis (HP:0000804)

Input	HPO ID	HPO term	Distance	Gene	Gene id entrez	HGNC ID	DiseaseId	DiseaseName	Frequency	ClinVar variants
HPO disease - gene - phenotype typical associations:
HPO disease - gene - phenotype less frequent non-typical associations:
HP:0004724	HP:0004724	Calcium nephrolithiasis	0	ADCY10 CL E G H	55811	21285	OMIM:143870	Hypercalciuria, absorptive, susceptibility to		5
HP:0004724	HP:0004724	Calcium nephrolithiasis	0	ADCY10 CL E G H	55811	21285	ORPHA:2197	Idiopathic hypercalciuria		5
HP:0004724	HP:0004724	Calcium nephrolithiasis	0	AGXT CL E G H	189	341	OMIM:259900	Hyperoxaluria, primary, type I		260
HP:0004724	HP:0004724	Calcium nephrolithiasis	0	GRHPR CL E G H	9380	4570	OMIM:260000	Hyperoxaluria, primary, type II		70
HP:0004724	HP:0004724	Calcium nephrolithiasis	0	HOGA1 CL E G H	112817	25155	OMIM:613616	HYPEROXALURIA, PRIMARY, TYPE III; HP3		83
HP:0004724	HP:0004724	Calcium nephrolithiasis	0	HOGA1 CL E G H	112817	25155	ORPHA:93600	Primary hyperoxaluria type 3		83
HP:0004724	HP:0004724	Calcium nephrolithiasis	0	OPLAH CL E G H	26873	8149	OMIM:260005	5-@oxoprolinase deficiency		5
HP:0004724	HP:0004724	Calcium nephrolithiasis	0	SLC26A1 CL E G H	10861	10993	OMIM:167030	Nephrolithiasis, calcium oxalate		24
HP:0004724	HP:0004724	Calcium nephrolithiasis	0	SLC34A2 CL E G H	10568	11020	ORPHA:60025	Pulmonary alveolar microlithiasis	HP:0040284 - Very rare	7
HP:0004724	HP:0004724	Calcium nephrolithiasis	0	SLC34A3 CL E G H	142680	20305	OMIM:241530	Hypophosphatemic rickets with hypercalciuria, hereditary	.	52
HP:0004724	HP:0004724	Calcium nephrolithiasis	0	SLC36A2 CL E G H	153201	18762	OMIM:138500	Glycinuria with or without oxalate urolithiasis		2
HP:0004724	HP:0004724	Calcium nephrolithiasis	0	SLC6A19 CL E G H	340024	27960	OMIM:138500	Glycinuria with or without oxalate urolithiasis		12
HP:0004724	HP:0004724	Calcium nephrolithiasis	0	SLC6A20 CL E G H	54716	30927	OMIM:138500	Glycinuria with or without oxalate urolithiasis		96
HP:0004724	HP:0012580	Calcium phosphate nephrolithiasis	1	CL E G H
HP:0004724	HP:0008672	Calcium oxalate nephrolithiasis	1	ADCY10 CL E G H	55811	21285	OMIM:143870	Hypercalciuria, absorptive, susceptibility to	.	5
HP:0004724	HP:0008672	Calcium oxalate nephrolithiasis	1	ADCY10 CL E G H	55811	21285	ORPHA:2197	Idiopathic hypercalciuria	HP:0040282 - Frequent	5
HP:0004724	HP:0008672	Calcium oxalate nephrolithiasis	1	AGXT CL E G H	189	341	OMIM:259900	Hyperoxaluria, primary, type I	.	260
HP:0004724	HP:0008672	Calcium oxalate nephrolithiasis	1	GRHPR CL E G H	9380	4570	OMIM:260000	Hyperoxaluria, primary, type II	.	70
HP:0004724	HP:0008672	Calcium oxalate nephrolithiasis	1	HOGA1 CL E G H	112817	25155	OMIM:613616	HYPEROXALURIA, PRIMARY, TYPE III; HP3		83
HP:0004724	HP:0008672	Calcium oxalate nephrolithiasis	1	HOGA1 CL E G H	112817	25155	ORPHA:93600	Primary hyperoxaluria type 3	HP:0040281 - Very frequent	83
HP:0004724	HP:0008672	Calcium oxalate nephrolithiasis	1	OPLAH CL E G H	26873	8149	OMIM:260005	5-@oxoprolinase deficiency	.	5
HP:0004724	HP:0008672	Calcium oxalate nephrolithiasis	1	SLC26A1 CL E G H	10861	10993	OMIM:167030	Nephrolithiasis, calcium oxalate	.	24
HP:0004724	HP:0008672	Calcium oxalate nephrolithiasis	1	SLC36A2 CL E G H	153201	18762	OMIM:138500	Glycinuria with or without oxalate urolithiasis	.	2
HP:0004724	HP:0008672	Calcium oxalate nephrolithiasis	1	SLC6A19 CL E G H	340024	27960	OMIM:138500	Glycinuria with or without oxalate urolithiasis	.	12
HP:0004724	HP:0008672	Calcium oxalate nephrolithiasis	1	SLC6A20 CL E G H	54716	30927	OMIM:138500	Glycinuria with or without oxalate urolithiasis	.	96

Genes (11) :ADCY10 AGXT GRHPR HOGA1 OPLAH SLC26A1 SLC34A2 SLC34A3 SLC36A2 SLC6A19 SLC6A20

Diseases (11) :OMIM:143870 ORPHA:2197 OMIM:259900 OMIM:260000 OMIM:613616 ORPHA:93600 OMIM:260005 OMIM:167030 ORPHA:60025 OMIM:241530 OMIM:138500

Human Phenotype Ontology(HPO) is developed by the Human Phenotype Ontology Consortium. The version used here is December 15 2022 release.

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