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:
Abnormality of urine homeostasis (HP:0003110)

Parent Node:
Abnormal urinary color (HP:0012086)

..Starting node
..Dark urine (HP:0040319)

Term ID:

40319

Name:

Dark urine

Synonym:

Definition:

An abnormal dark color of the urine.

Comments:

Reference:

HP:0040319

Genes and Diseases:

Child Nodes:

Sister Nodes:

Blue urine (HP:0040317)

Dark yellow urine (HP:0040321)

Purple urine (HP:0040322)

Red urine (HP:0040318)

Red-brown urine (HP:0040320)

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:0040319	HP:0040319	Dark urine	0	AKR1D1 CL E G H	6718	388	ORPHA:79303	Congenital bile acid synthesis defect type 2		62
HP:0040319	HP:0040319	Dark urine	0	ATP11C CL E G H	286410	13554	OMIM:301015	Hemolytic anemia, congenital, X-linked		1
HP:0040319	HP:0040319	Dark urine	0	COX1 CL E G H	4512	7419	ORPHA:99845	Genetic recurrent myoglobinuria
HP:0040319	HP:0040319	Dark urine	0	COX3 CL E G H	4514	7422	ORPHA:99845	Genetic recurrent myoglobinuria
HP:0040319	HP:0040319	Dark urine	0	CPOX CL E G H	1371	2321	ORPHA:79273	Hereditary coproporphyria	HP:0040282 - Frequent	72
HP:0040319	HP:0040319	Dark urine	0	HMBS CL E G H	3145	4982	ORPHA:79276	Acute intermittent porphyria	HP:0040283 - Occasional	81
HP:0040319	HP:0040319	Dark urine	0	IRAK1 CL E G H	3654	6112	ORPHA:93552	Pediatric systemic lupus erythematosus	HP:0040283 - Occasional
HP:0040319	HP:0040319	Dark urine	0	LPIN1 CL E G H	23175	13345	ORPHA:99845	Genetic recurrent myoglobinuria		95
HP:0040319	HP:0040319	Dark urine	0	PYGM CL E G H	5837	9726	ORPHA:368	Glycogen storage disease due to muscle glycogen phosphorylase deficiency	HP:0040282 - Frequent	166
HP:0040319	HP:0040319	Dark urine	0	PYGM CL E G H	5837	9726	OMIM:232600	Glycogen storage disease V	.	166
HP:0040319	HP:0040319	Dark urine	0	SPP1 CL E G H	6696	11255	ORPHA:93552	Pediatric systemic lupus erythematosus	HP:0040283 - Occasional
HP:0040319	HP:0040319	Dark urine	0	STAT4 CL E G H	6775	11365	ORPHA:93552	Pediatric systemic lupus erythematosus	HP:0040283 - Occasional	2
HP:0040319	HP:0040319	Dark urine	0	TTC26 CL E G H	79989	21882	OMIM:619534	BILIARY, RENAL, NEUROLOGIC, AND SKELETAL SYNDROME; BRENS

Genes (12) :AKR1D1 ATP11C COX1 COX3 CPOX HMBS IRAK1 LPIN1 PYGM SPP1 STAT4 TTC26

Diseases (9) :ORPHA:79303 OMIM:301015 ORPHA:99845 ORPHA:79273 ORPHA:79276 ORPHA:93552 ORPHA:368 OMIM:232600 OMIM:619534

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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