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 the biliary system (HP:0004297)

Parent Node:
Abnormal liver physiology (HP:0031865)

Parent Node:
Cholestasis (HP:0001396)

..Starting node
..Intrahepatic cholestasis (HP:0001406)

Term ID:

1406

Name:

Intrahepatic cholestasis

Synonym:

Impaired release of bile from liver

Definition:

Impairment of bile flow due to obstruction in the small bile ducts within the liver.

Comments:

Reference:

HP:0001406

Genes and Diseases:

Child Nodes:

........

Intrahepatic cholestasis with episodic jaundice (HP:0006575)

Sister Nodes:

Acholic stools (HP:0011985)

Cholestatic liver disease (HP:0002611)

Extrahepatic cholestasis (HP:0012334)

Jaundice (HP:0000952)

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:0001406	HP:0001406	Intrahepatic cholestasis	0	ABCB11 CL E G H	8647	42	OMIM:605479	Cholestasis, benign recurrent intrahepatic, 2	HP:0040283 - Occasional	146
HP:0001406	HP:0001406	Intrahepatic cholestasis	0	ABCB11 CL E G H	8647	42	OMIM:601847	Cholestasis, progressive familial intrahepatic 2	.	146
HP:0001406	HP:0001406	Intrahepatic cholestasis	0	ABCB4 CL E G H	5244	45	OMIM:614972	Cholestasis, intrahepatic, of pregnancy 3	.	111
HP:0001406	HP:0001406	Intrahepatic cholestasis	0	ABCB4 CL E G H	5244	45	OMIM:602347	Cholestasis, progressive familial intrahepatic, 3	.	111
HP:0001406	HP:0001406	Intrahepatic cholestasis	0	ABCB4 CL E G H	5244	45	ORPHA:69663	Low phospholipid-associated cholelithiasis	HP:0040281 - Very frequent	111
HP:0001406	HP:0001406	Intrahepatic cholestasis	0	AKR1D1 CL E G H	6718	388	OMIM:235555	Bile acid synthesis defect, congenital, 2	.	62
HP:0001406	HP:0001406	Intrahepatic cholestasis	0	AMACR CL E G H	23600	451	OMIM:214950	Bile acid synthesis defect, congenital, 4	.	44
HP:0001406	HP:0001406	Intrahepatic cholestasis	0	AP1B1 CL E G H	162	554	ORPHA:171851	MEDNIK syndrome	HP:0040282 - Frequent
HP:0001406	HP:0001406	Intrahepatic cholestasis	0	AP1S1 CL E G H	1174	559	ORPHA:171851	MEDNIK syndrome	HP:0040282 - Frequent	1
HP:0001406	HP:0001406	Intrahepatic cholestasis	0	ASAH1 CL E G H	427	735	ORPHA:333	Farber disease		78
HP:0001406	HP:0001406	Intrahepatic cholestasis	0	ATP8B1 CL E G H	5205	3706	OMIM:243300	Cholestasis, benign recurrent intrahepatic 1		144
HP:0001406	HP:0001406	Intrahepatic cholestasis	0	ATP8B1 CL E G H	5205	3706	OMIM:147480	Cholestasis, intrahepatic, of pregnancy, 1	.	144
HP:0001406	HP:0001406	Intrahepatic cholestasis	0	ATP8B1 CL E G H	5205	3706	OMIM:211600	Cholestasis, progressive familial intrahepatic 1		144
HP:0001406	HP:0001406	Intrahepatic cholestasis	0	CYP7B1 CL E G H	9420	2652	OMIM:613812	Bile acid synthesis defect, congenital, 3	.	57
HP:0001406	HP:0001406	Intrahepatic cholestasis	0	FOCAD CL E G H	54914	23377	OMIM:619991			3
HP:0001406	HP:0001406	Intrahepatic cholestasis	0	HSD3B7 CL E G H	80270	18324	OMIM:607765	Bile acid synthesis defect, congenital, 1	.	26
HP:0001406	HP:0001406	Intrahepatic cholestasis	0	PGM1 CL E G H	5236	8905	OMIM:614921	Congenital disorder of glycosylation, type It		58
HP:0001406	HP:0001406	Intrahepatic cholestasis	0	PKHD1 CL E G H	5314	9016	ORPHA:53035	Caroli disease	HP:0040282 - Frequent	563
HP:0001406	HP:0001406	Intrahepatic cholestasis	0	SC5D CL E G H	6309	10547	ORPHA:46059	Lathosterolosis	HP:0040282 - Frequent	80
HP:0001406	HP:0001406	Intrahepatic cholestasis	0	SC5D CL E G H	6309	10547	OMIM:607330	LATHOSTEROLOSIS		80
HP:0001406	HP:0001406	Intrahepatic cholestasis	0	SLC25A13 CL E G H	10165	10983	OMIM:605814	Citrullinemia, type II, neonatal-onset	.	82
HP:0001406	HP:0001406	Intrahepatic cholestasis	0	SLC51A CL E G H	200931	29955	OMIM:619484	CHOLESTASIS, PROGRESSIVE FAMILIAL INTRAHEPATIC, 6; PFIC6
HP:0001406	HP:0001406	Intrahepatic cholestasis	0	TJP2 CL E G H	9414	11828	OMIM:615878	CHOLESTASIS, PROGRESSIVE FAMILIAL INTRAHEPATIC, 4; PFIC4		149
HP:0001406	HP:0001406	Intrahepatic cholestasis	0	TMPRSS6 CL E G H	164656	16517	ORPHA:209981	IRIDA syndrome	HP:0040282 - Frequent	65
HP:0001406	HP:0001406	Intrahepatic cholestasis	0	VPS50 CL E G H	55610	25956	OMIM:619685	NEURODEVELOPMENTAL DISORDER WITH MICROCEPHALY, SEIZURES, AND NEONATAL CHOLESTASIS; NEDMSC
HP:0001406	HP:0001406	Intrahepatic cholestasis	0	ZFYVE19 CL E G H	84936	20758	OMIM:619849
HP:0001406	HP:0006575	Intrahepatic cholestasis with episodic jaundice	1	ASAH1 CL E G H	427	735	ORPHA:333	Farber disease	HP:0040284 - Very rare	78
HP:0001406	HP:0006575	Intrahepatic cholestasis with episodic jaundice	1	ATP8B1 CL E G H	5205	3706	OMIM:243300	Cholestasis, benign recurrent intrahepatic 1	.	144
HP:0001406	HP:0006575	Intrahepatic cholestasis with episodic jaundice	1	ATP8B1 CL E G H	5205	3706	OMIM:211600	Cholestasis, progressive familial intrahepatic 1	.	144

Genes (20) :ABCB11 ABCB4 AKR1D1 AMACR AP1B1 AP1S1 ASAH1 ATP8B1 CYP7B1 FOCAD HSD3B7 PGM1 PKHD1 SC5D SLC25A13 SLC51A TJP2 TMPRSS6 VPS50 ZFYVE19

Diseases (25) :OMIM:605479 OMIM:601847 OMIM:614972 OMIM:602347 ORPHA:69663 OMIM:235555 OMIM:214950 ORPHA:171851 ORPHA:333 OMIM:243300 OMIM:147480 OMIM:211600 OMIM:613812 OMIM:619991 OMIM:607765 OMIM:614921 ORPHA:53035 ORPHA:46059 OMIM:607330 OMIM:605814 OMIM:619484 OMIM:615878 ORPHA:209981 OMIM:619685 OMIM:619849

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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