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 gallbladder (HP:0005264)

Parent Node:
Abnormal gallbladder morphology (HP:0012437)

..Starting node
..Cholelithiasis (HP:0001081)

Term ID:

1081

Name:

Cholelithiasis

Synonym:

Gallstones

Definition:

Hard, pebble-like deposits that form within the gallbladder.

Comments:

Reference:

HP:0001081

Genes and Diseases:

Child Nodes:

........

Cholesterol gallstones (HP:0011980)

........

Pigment gallstones (HP:0011981)

................... HP:0011982 Black pigment gallstones
................... HP:0011983 Brown pigment gallstones

Sister Nodes:

Aplasia/Hypoplasia of the gallbladder (HP:0011466)

Bilobate gallbladder (HP:0005608)

Cystic artery pseudoaneurysm (HP:0030170)

Gallbladder perforation (HP:0030154)

Neoplasm of the gallbladder (HP:0100575)

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:0001081	HP:0001081	Cholelithiasis	0	ABCB11 CL E G H	8647	42	OMIM:605479	Cholestasis, benign recurrent intrahepatic, 2	.	146
HP:0001081	HP:0001081	Cholelithiasis	0	ABCB4 CL E G H	5244	45	OMIM:600803	Gallbladder disease 1	.	111
HP:0001081	HP:0001081	Cholelithiasis	0	ABCB4 CL E G H	5244	45	ORPHA:69663	Low phospholipid-associated cholelithiasis	HP:0040282 - Frequent	111
HP:0001081	HP:0001081	Cholelithiasis	0	ABCG8 CL E G H	64241	13887	OMIM:611465	GALLBLADDER DISEASE 4; GBD4		76
HP:0001081	HP:0001081	Cholelithiasis	0	ACVRL1 CL E G H	94	175	ORPHA:774	Hereditary hemorrhagic telangiectasia	HP:0040283 - Occasional	178
HP:0001081	HP:0001081	Cholelithiasis	0	AIRE CL E G H	326	360	OMIM:240300	AUTOIMMUNE POLYENDOCRINE SYNDROME, TYPE I, WITH OR WITHOUT REVERSIBLE METAPHYSEAL DYSPLASIA; APS1		92
HP:0001081	HP:0001081	Cholelithiasis	0	ALAS2 CL E G H	212	397	OMIM:300752	Protoporphyria, erythropoietic, X-linked	HP:0040283 - Occasional	72
HP:0001081	HP:0001081	Cholelithiasis	0	ALDOA CL E G H	226	414	OMIM:611881	Glycogen storage disease XII	.	50
HP:0001081	HP:0001081	Cholelithiasis	0	AMACR CL E G H	23600	451	ORPHA:79095	Congenital bile acid synthesis defect type 4		44
HP:0001081	HP:0001081	Cholelithiasis	0	ANK1 CL E G H	286	492	ORPHA:822	Hereditary spherocytosis	HP:0040282 - Frequent	150
HP:0001081	HP:0001081	Cholelithiasis	0	ANK1 CL E G H	286	492	OMIM:182900	Spherocytosis, type 1	.	150
HP:0001081	HP:0001081	Cholelithiasis	0	ARVCF CL E G H	421	728	ORPHA:567	22q11.2 deletion syndrome	HP:0040283 - Occasional	1
HP:0001081	HP:0001081	Cholelithiasis	0	ASXL1 CL E G H	171023	18318	ORPHA:97297	Bohring-Opitz syndrome	HP:0040284 - Very rare	145
HP:0001081	HP:0001081	Cholelithiasis	0	ATP8B1 CL E G H	5205	3706	OMIM:211600	Cholestasis, progressive familial intrahepatic 1		144
HP:0001081	HP:0001081	Cholelithiasis	0	BAZ1B CL E G H	9031	961	ORPHA:904	Williams syndrome	HP:0040283 - Occasional
HP:0001081	HP:0001081	Cholelithiasis	0	BCL7B CL E G H	9275	1005	ORPHA:904	Williams syndrome	HP:0040283 - Occasional
HP:0001081	HP:0001081	Cholelithiasis	0	BLVRA CL E G H	644	1062	OMIM:614156	Hyperbiliverdinemia	.	2
HP:0001081	HP:0001081	Cholelithiasis	0	BUD23 CL E G H	114049	16405	ORPHA:904	Williams syndrome	HP:0040283 - Occasional
HP:0001081	HP:0001081	Cholelithiasis	0	CCDC47 CL E G H	57003	24856	OMIM:618268	Trichohepatoneurodevelopmental syndrome	HP:0040284 - Very rare
HP:0001081	HP:0001081	Cholelithiasis	0	CLIP2 CL E G H	7461	2586	ORPHA:904	Williams syndrome	HP:0040283 - Occasional
HP:0001081	HP:0001081	Cholelithiasis	0	COMT CL E G H	1312	2228	ORPHA:567	22q11.2 deletion syndrome	HP:0040283 - Occasional	6
HP:0001081	HP:0001081	Cholelithiasis	0	CYP27A1 CL E G H	1593	2605	ORPHA:909	Cerebrotendinous xanthomatosis	HP:0040283 - Occasional	114
HP:0001081	HP:0001081	Cholelithiasis	0	CYP27A1 CL E G H	1593	2605	OMIM:213700	Cerebrotendinous xanthomatosis		114
HP:0001081	HP:0001081	Cholelithiasis	0	CYP7A1 CL E G H	1581	2651	ORPHA:209902	Hypercholesterolemia due to cholesterol 7alpha-hydroxylase deficiency		11
HP:0001081	HP:0001081	Cholelithiasis	0	DMPK CL E G H	1760	2933	OMIM:160900	Myotonic dystrophy 1	.	152
HP:0001081	HP:0001081	Cholelithiasis	0	DNAJC30 CL E G H	84277	16410	ORPHA:904	Williams syndrome	HP:0040283 - Occasional
HP:0001081	HP:0001081	Cholelithiasis	0	EIF4H CL E G H	7458	12741	ORPHA:904	Williams syndrome	HP:0040283 - Occasional
HP:0001081	HP:0001081	Cholelithiasis	0	ELN CL E G H	2006	3327	ORPHA:904	Williams syndrome	HP:0040283 - Occasional	172
HP:0001081	HP:0001081	Cholelithiasis	0	ENG CL E G H	2022	3349	ORPHA:774	Hereditary hemorrhagic telangiectasia	HP:0040283 - Occasional	186
HP:0001081	HP:0001081	Cholelithiasis	0	EPB41 CL E G H	2035	3377	ORPHA:288	Hereditary elliptocytosis	HP:0040284 - Very rare	6
HP:0001081	HP:0001081	Cholelithiasis	0	EPB42 CL E G H	2038	3381	ORPHA:822	Hereditary spherocytosis	HP:0040282 - Frequent	51
HP:0001081	HP:0001081	Cholelithiasis	0	FECH CL E G H	2235	3647	ORPHA:79278	Autosomal erythropoietic protoporphyria	HP:0040283 - Occasional	145
HP:0001081	HP:0001081	Cholelithiasis	0	FECH CL E G H	2235	3647	OMIM:177000	Protoporphyria, erythropoietic, 1	.	145
HP:0001081	HP:0001081	Cholelithiasis	0	FKBP6 CL E G H	8468	3722	ORPHA:904	Williams syndrome	HP:0040283 - Occasional
HP:0001081	HP:0001081	Cholelithiasis	0	GBA1 CL E G H	2629	4177	ORPHA:2072	Gaucher disease-ophthalmoplegia-cardiovascular calcification syndrome	HP:0040284 - Very rare
HP:0001081	HP:0001081	Cholelithiasis	0	GCGR CL E G H	2642	4192	ORPHA:438274	GCGR-related hyperglucagonemia	HP:0040282 - Frequent	1
HP:0001081	HP:0001081	Cholelithiasis	0	GDF2 CL E G H	2658	4217	ORPHA:774	Hereditary hemorrhagic telangiectasia	HP:0040283 - Occasional	8
HP:0001081	HP:0001081	Cholelithiasis	0	GNE CL E G H	10020	23657	ORPHA:3166	Sialuria	HP:0040281 - Very frequent	173
HP:0001081	HP:0001081	Cholelithiasis	0	GP1BB CL E G H	2812	4440	ORPHA:567	22q11.2 deletion syndrome	HP:0040283 - Occasional	8
HP:0001081	HP:0001081	Cholelithiasis	0	GPI CL E G H	2821	4458	OMIM:613470	Hemolytic anemia, nonspherocytic, due to glucose phosphate isomerasedeficiency	.	12
HP:0001081	HP:0001081	Cholelithiasis	0	GPR35 CL E G H	2859	4492	ORPHA:171	Primary sclerosing cholangitis	HP:0040283 - Occasional	2
HP:0001081	HP:0001081	Cholelithiasis	0	GTF2I CL E G H	2969	4659	ORPHA:904	Williams syndrome	HP:0040283 - Occasional	1
HP:0001081	HP:0001081	Cholelithiasis	0	GTF2IRD1 CL E G H	9569	4661	ORPHA:904	Williams syndrome	HP:0040283 - Occasional	1
HP:0001081	HP:0001081	Cholelithiasis	0	GTF2IRD2 CL E G H	84163	30775	ORPHA:904	Williams syndrome	HP:0040283 - Occasional	1
HP:0001081	HP:0001081	Cholelithiasis	0	GYPC CL E G H	2995	4704	ORPHA:288	Hereditary elliptocytosis	HP:0040284 - Very rare	5
HP:0001081	HP:0001081	Cholelithiasis	0	HBB CL E G H	3043	4827	ORPHA:231222	Beta-thalassemia intermedia	HP:0040283 - Occasional	580
HP:0001081	HP:0001081	Cholelithiasis	0	HBB CL E G H	3043	4827	OMIM:603903	Sickle cell anemia	.	580
HP:0001081	HP:0001081	Cholelithiasis	0	HBB CL E G H	3043	4827	ORPHA:232	Sickle cell anemia		580
HP:0001081	HP:0001081	Cholelithiasis	0	HIRA CL E G H	7290	4916	ORPHA:567	22q11.2 deletion syndrome	HP:0040283 - Occasional	3
HP:0001081	HP:0001081	Cholelithiasis	0	HK1 CL E G H	3098	4922	OMIM:235700	Hemolytic anemia, nonspherocytic, due to hexokinase deficiency	.	11
HP:0001081	HP:0001081	Cholelithiasis	0	JMJD1C CL E G H	221037	12313	ORPHA:567	22q11.2 deletion syndrome	HP:0040283 - Occasional	2
HP:0001081	HP:0001081	Cholelithiasis	0	KCNN4 CL E G H	3783	6293	ORPHA:3202	Dehydrated hereditary stomatocytosis	HP:0040282 - Frequent	3
HP:0001081	HP:0001081	Cholelithiasis	0	KDM5C CL E G H	8242	11114	OMIM:300534	Mental retardation, X-linked, syndromic, Claes-Jensen type		81
HP:0001081	HP:0001081	Cholelithiasis	0	LIMK1 CL E G H	3984	6613	ORPHA:904	Williams syndrome	HP:0040283 - Occasional
HP:0001081	HP:0001081	Cholelithiasis	0	MED25 CL E G H	81857	28845	ORPHA:464738	Basel-Vanagaite-Smirin-Yosef syndrome	HP:0040283 - Occasional	43
HP:0001081	HP:0001081	Cholelithiasis	0	METTL27 CL E G H	155368	19068	ORPHA:904	Williams syndrome	HP:0040283 - Occasional	1
HP:0001081	HP:0001081	Cholelithiasis	0	MLXIPL CL E G H	51085	12744	ORPHA:904	Williams syndrome	HP:0040283 - Occasional	1
HP:0001081	HP:0001081	Cholelithiasis	0	MST1 CL E G H	4485	7380	ORPHA:171	Primary sclerosing cholangitis	HP:0040283 - Occasional	1
HP:0001081	HP:0001081	Cholelithiasis	0	NCF1 CL E G H	653361	7660	ORPHA:904	Williams syndrome	HP:0040283 - Occasional	13
HP:0001081	HP:0001081	Cholelithiasis	0	PEX19 CL E G H	5824	9713	OMIM:614886	Peroxisome biogenesis disorder 12A (Zellweger)	.	62
HP:0001081	HP:0001081	Cholelithiasis	0	PFKM CL E G H	5213	8877	OMIM:232800	Glycogen storage disease VII	.	64
HP:0001081	HP:0001081	Cholelithiasis	0	PIEZO1 CL E G H	9780	28993	ORPHA:3202	Dehydrated hereditary stomatocytosis	HP:0040282 - Frequent	36
HP:0001081	HP:0001081	Cholelithiasis	0	PIEZO1 CL E G H	9780	28993	OMIM:194380	Dehydrated hereditary stomatocytosis 1 with or without pseudohyperkalemia and/or perinatal edema	HP:0040283 - Occasional	36
HP:0001081	HP:0001081	Cholelithiasis	0	PKHD1 CL E G H	5314	9016	ORPHA:53035	Caroli disease	HP:0040283 - Occasional	563
HP:0001081	HP:0001081	Cholelithiasis	0	PKLR CL E G H	5313	9020	OMIM:266200	Pyruvate kinase deficiency of red cells	.	51
HP:0001081	HP:0001081	Cholelithiasis	0	RFC2 CL E G H	5982	9970	ORPHA:904	Williams syndrome	HP:0040283 - Occasional
HP:0001081	HP:0001081	Cholelithiasis	0	RREB1 CL E G H	6239	10449	ORPHA:567	22q11.2 deletion syndrome	HP:0040283 - Occasional
HP:0001081	HP:0001081	Cholelithiasis	0	SCNN1A CL E G H	6337	10599	ORPHA:171876	Generalized pseudohypoaldosteronism type 1	HP:0040283 - Occasional	67
HP:0001081	HP:0001081	Cholelithiasis	0	SCNN1B CL E G H	6338	10600	ORPHA:171876	Generalized pseudohypoaldosteronism type 1	HP:0040283 - Occasional	61
HP:0001081	HP:0001081	Cholelithiasis	0	SCNN1G CL E G H	6340	10602	ORPHA:171876	Generalized pseudohypoaldosteronism type 1	HP:0040283 - Occasional	57
HP:0001081	HP:0001081	Cholelithiasis	0	SEC23B CL E G H	10483	10702	OMIM:224100	Anemia, dyserythropoietic congenital, type II	.	60
HP:0001081	HP:0001081	Cholelithiasis	0	SEC24C CL E G H	9632	10705	ORPHA:567	22q11.2 deletion syndrome	HP:0040283 - Occasional
HP:0001081	HP:0001081	Cholelithiasis	0	SEMA4D CL E G H	10507	10732	ORPHA:171	Primary sclerosing cholangitis	HP:0040283 - Occasional
HP:0001081	HP:0001081	Cholelithiasis	0	SLC4A1 CL E G H	6521	11027	ORPHA:3202	Dehydrated hereditary stomatocytosis	HP:0040282 - Frequent	109
HP:0001081	HP:0001081	Cholelithiasis	0	SLC4A1 CL E G H	6521	11027	ORPHA:822	Hereditary spherocytosis	HP:0040282 - Frequent	109
HP:0001081	HP:0001081	Cholelithiasis	0	SMAD4 CL E G H	4089	6770	ORPHA:774	Hereditary hemorrhagic telangiectasia	HP:0040283 - Occasional	504
HP:0001081	HP:0001081	Cholelithiasis	0	SMPD1 CL E G H	6609	11120	ORPHA:77293	Niemann-Pick disease type B	HP:0040284 - Very rare	164
HP:0001081	HP:0001081	Cholelithiasis	0	SPTA1 CL E G H	6708	11272	ORPHA:288	Hereditary elliptocytosis	HP:0040284 - Very rare	228
HP:0001081	HP:0001081	Cholelithiasis	0	SPTA1 CL E G H	6708	11272	ORPHA:822	Hereditary spherocytosis	HP:0040282 - Frequent	228
HP:0001081	HP:0001081	Cholelithiasis	0	SPTB CL E G H	6710	11274	ORPHA:288	Hereditary elliptocytosis	HP:0040284 - Very rare	156
HP:0001081	HP:0001081	Cholelithiasis	0	SPTB CL E G H	6710	11274	ORPHA:822	Hereditary spherocytosis	HP:0040282 - Frequent	156
HP:0001081	HP:0001081	Cholelithiasis	0	STX1A CL E G H	6804	11433	ORPHA:904	Williams syndrome	HP:0040283 - Occasional
HP:0001081	HP:0001081	Cholelithiasis	0	TBL2 CL E G H	26608	11586	ORPHA:904	Williams syndrome	HP:0040283 - Occasional
HP:0001081	HP:0001081	Cholelithiasis	0	TBX1 CL E G H	6899	11592	ORPHA:567	22q11.2 deletion syndrome	HP:0040283 - Occasional	32
HP:0001081	HP:0001081	Cholelithiasis	0	TBX1 CL E G H	6899	11592	OMIM:188400	Digeorge syndrome	.	32
HP:0001081	HP:0001081	Cholelithiasis	0	TCF4 CL E G H	6925	11634	ORPHA:171	Primary sclerosing cholangitis	HP:0040283 - Occasional	241
HP:0001081	HP:0001081	Cholelithiasis	0	TFE3 CL E G H	7030	11752	OMIM:301066	INTELLECTUAL DEVELOPMENTAL DISORDER, X-LINKED, SYNDROMIC, WITH PIGMENTARY MOSAICISM AND COARSE FACIES; MRXSPF
HP:0001081	HP:0001081	Cholelithiasis	0	TMEM270 CL E G H	135886	23018	ORPHA:904	Williams syndrome	HP:0040283 - Occasional
HP:0001081	HP:0001081	Cholelithiasis	0	TPI1 CL E G H	7167	12009	OMIM:615512	Triosephosphate isomerase deficiency	.	28
HP:0001081	HP:0001081	Cholelithiasis	0	UFD1 CL E G H	7353	12520	ORPHA:567	22q11.2 deletion syndrome	HP:0040283 - Occasional
HP:0001081	HP:0001081	Cholelithiasis	0	UQCRFS1 CL E G H	7386	12587	OMIM:618775	MITOCHONDRIAL COMPLEX III DEFICIENCY, NUCLEAR TYPE 10; MC3DN10
HP:0001081	HP:0001081	Cholelithiasis	0	UROS CL E G H	7390	12592	OMIM:263700	Porphyria, congenital erythropoietic	.	41
HP:0001081	HP:0001081	Cholelithiasis	0	VPS37D CL E G H	155382	18287	ORPHA:904	Williams syndrome	HP:0040283 - Occasional
HP:0001081	HP:0001081	Cholelithiasis	0	VPS4A CL E G H	27183	13488	OMIM:619273	CIMDAG SYNDROME; CIMDAG		1
HP:0001081	HP:0011980	Cholesterol gallstones	1	ABCB4 CL E G H	5244	45	OMIM:600803	Gallbladder disease 1	.	111
HP:0001081	HP:0011980	Cholesterol gallstones	1	CYP7A1 CL E G H	1581	2651	ORPHA:209902	Hypercholesterolemia due to cholesterol 7alpha-hydroxylase deficiency	HP:0040281 - Very frequent	11
HP:0001081	HP:0011981	Pigment gallstones	1	GPI CL E G H	2821	4458	OMIM:613470	Hemolytic anemia, nonspherocytic, due to glucose phosphate isomerasedeficiency	.	12
HP:0001081	HP:0011981	Pigment gallstones	1	HBB CL E G H	3043	4827	ORPHA:232	Sickle cell anemia	HP:0040282 - Frequent	580
HP:0001081	HP:0011982	Black pigment gallstones	2	CL E G H
HP:0001081	HP:0011983	Brown pigment gallstones	2	CL E G H

Genes (83) :ABCB11 ABCB4 ABCG8 ACVRL1 AIRE ALAS2 ALDOA AMACR ANK1 ARVCF ASXL1 ATP8B1 BAZ1B BCL7B BLVRA BUD23 CCDC47 CLIP2 COMT CYP27A1 CYP7A1 DMPK DNAJC30 EIF4H ELN ENG EPB41 EPB42 FECH FKBP6 GBA1 GCGR GDF2 GNE GP1BB GPI GPR35 GTF2I GTF2IRD1 GTF2IRD2 GYPC HBB HIRA HK1 JMJD1C KCNN4 KDM5C LIMK1 MED25 METTL27 MLXIPL MST1 NCF1 PEX19 PFKM PIEZO1 PKHD1 PKLR RFC2 RREB1 SCNN1A SCNN1B SCNN1G SEC23B SEC24C SEMA4D SLC4A1 SMAD4 SMPD1 SPTA1 SPTB STX1A TBL2 TBX1 TCF4 TFE3 TMEM270 TPI1 UFD1 UQCRFS1 UROS VPS37D VPS4A

Diseases (50) :OMIM:605479 OMIM:600803 ORPHA:69663 OMIM:611465 ORPHA:774 OMIM:240300 OMIM:300752 OMIM:611881 ORPHA:79095 ORPHA:822 OMIM:182900 ORPHA:567 ORPHA:97297 OMIM:211600 ORPHA:904 OMIM:614156 OMIM:618268 ORPHA:909 OMIM:213700 ORPHA:209902 OMIM:160900 ORPHA:288 ORPHA:79278 OMIM:177000 ORPHA:2072 ORPHA:438274 ORPHA:3166 OMIM:613470 ORPHA:171 ORPHA:231222 OMIM:603903 ORPHA:232 OMIM:235700 ORPHA:3202 OMIM:300534 ORPHA:464738 OMIM:614886 OMIM:232800 OMIM:194380 ORPHA:53035 OMIM:266200 ORPHA:171876 OMIM:224100 ORPHA:77293 OMIM:188400 OMIM:301066 OMIM:615512 OMIM:618775 OMIM:263700 OMIM:619273

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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