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 small intestine (HP:0002244)

Parent Node:
Abnormality of small intestinal villus morphology (HP:0011472)

..Starting node
..Villous atrophy (HP:0011473)

Term ID:

11473

Name:

Villous atrophy

Synonym:

Atrophy of small intestinal villi; Biopsy shows villous atrophy; Duodenal villous atrophy; Small intestine biopsy shows villous atrophy; Variable degree of villous atrophy; Villous degeneration

Definition:

The enteric villi are atrophic or absent.

Comments:

Reference:

HP:0011473

Genes and Diseases:

Child Nodes:

Sister Nodes:

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:0011473	HP:0011473	Villous atrophy	0	ADAM17 CL E G H	6868	195	OMIM:614328	INFLAMMATORY SKIN AND BOWEL DISEASE, NEONATAL, 1; NISBD1		2
HP:0011473	HP:0011473	Villous atrophy	0	ALG3 CL E G H	10195	23056	OMIM:601110	Congenital disorder of glycosylation, type Id	.	37
HP:0011473	HP:0011473	Villous atrophy	0	ALG9 CL E G H	79796	15672	ORPHA:79328	ALG9-CDG	HP:0040283 - Occasional	93
HP:0011473	HP:0011473	Villous atrophy	0	CIITA CL E G H	4261	7067	OMIM:209920	Bare lymphocyte syndrome, type II	.	118
HP:0011473	HP:0011473	Villous atrophy	0	DEF6 CL E G H	50619	2760	OMIM:619573	IMMUNODEFICIENCY 87 AND AUTOIMMUNITY; IMD87
HP:0011473	HP:0011473	Villous atrophy	0	DGAT1 CL E G H	8694	2843	OMIM:615863	Diarrhea 7, protein-losing Enteropathy type	.	9
HP:0011473	HP:0011473	Villous atrophy	0	EPCAM CL E G H	4072	11529	ORPHA:92050	Congenital tufting enteropathy	HP:0040281 - Very frequent	170
HP:0011473	HP:0011473	Villous atrophy	0	EPCAM CL E G H	4072	11529	OMIM:613217	Diarrhea 5, with tufting enteropathy, congenital	.	170
HP:0011473	HP:0011473	Villous atrophy	0	FOXP3 CL E G H	50943	6106	OMIM:304790	Immunodysregulation, polyendocrinopathy, and enteropathy, X-linked		32
HP:0011473	HP:0011473	Villous atrophy	0	IL2RA CL E G H	3559	6008	OMIM:606367	IMMUNODEFICIENCY 41 WITH LYMPHOPROLIFERATION AND AUTOIMMUNITY; IMD41		65
HP:0011473	HP:0011473	Villous atrophy	0	LRBA CL E G H	987	1742	OMIM:614700	IMMUNODEFICIENCY, COMMON VARIABLE, 8, WITH AUTOIMMUNITY; CVID8		45
HP:0011473	HP:0011473	Villous atrophy	0	MPI CL E G H	4351	7216	OMIM:602579	Congenital disorder of glycosylation, type Ib	.	51
HP:0011473	HP:0011473	Villous atrophy	0	MYO5B CL E G H	4645	7603	OMIM:251850	Diarrhea 2, with microvillous atrophy	.	192
HP:0011473	HP:0011473	Villous atrophy	0	MYO5B CL E G H	4645	7603	ORPHA:2290	Microvillus inclusion disease	HP:0040282 - Frequent	192
HP:0011473	HP:0011473	Villous atrophy	0	NLRC4 CL E G H	58484	16412	OMIM:616050	AUTOINFLAMMATION WITH INFANTILE ENTEROCOLITIS; AIFEC		30
HP:0011473	HP:0011473	Villous atrophy	0	PCSK1 CL E G H	5122	8743	OMIM:600955	Proprotein convertase 1/3 deficiency	.	65
HP:0011473	HP:0011473	Villous atrophy	0	PERCC1 CL E G H	105371045	52293	ORPHA:92050	Congenital tufting enteropathy	HP:0040281 - Very frequent
HP:0011473	HP:0011473	Villous atrophy	0	PERCC1 CL E G H	105371045	52293	OMIM:618662	DIARRHEA 11, MALABSORPTIVE, CONGENITAL; DIAR11
HP:0011473	HP:0011473	Villous atrophy	0	PMM2 CL E G H	5373	9115	OMIM:212065	Congenital disorder of glycosylation, type Ia		150
HP:0011473	HP:0011473	Villous atrophy	0	RFX5 CL E G H	5993	9986	OMIM:209920	Bare lymphocyte syndrome, type II	.	38
HP:0011473	HP:0011473	Villous atrophy	0	RFXANK CL E G H	8625	9987	OMIM:209920	Bare lymphocyte syndrome, type II	.	26
HP:0011473	HP:0011473	Villous atrophy	0	RFXAP CL E G H	5994	9988	OMIM:209920	Bare lymphocyte syndrome, type II	.	34
HP:0011473	HP:0011473	Villous atrophy	0	SKIC2 CL E G H	6499	10898	ORPHA:84064	Syndromic diarrhea	HP:0040282 - Frequent
HP:0011473	HP:0011473	Villous atrophy	0	SKIC2 CL E G H	6499	10898	OMIM:614602	Trichohepatoenteric syndrome 2	.
HP:0011473	HP:0011473	Villous atrophy	0	SKIC3 CL E G H	9652	23639	ORPHA:84064	Syndromic diarrhea	HP:0040282 - Frequent
HP:0011473	HP:0011473	Villous atrophy	0	SKIC3 CL E G H	9652	23639	OMIM:222470	Trichohepatoenteric syndrome 1
HP:0011473	HP:0011473	Villous atrophy	0	SPINK5 CL E G H	11005	15464	OMIM:256500	Netherton syndrome	.	100
HP:0011473	HP:0011473	Villous atrophy	0	STAT1 CL E G H	6772	11362	ORPHA:391487	Autoimmune enteropathy and endocrinopathy-susceptibility to chronic infections syndrome	HP:0040282 - Frequent	89
HP:0011473	HP:0011473	Villous atrophy	0	STAT1 CL E G H	6772	11362	OMIM:614162	Immunodeficiency 31C	HP:0040283 - Occasional	89
HP:0011473	HP:0011473	Villous atrophy	0	STX3 CL E G H	6809	11438	OMIM:619445	DIARRHEA 12, WITH MICROVILLUS ATROPHY; DIAR12		1
HP:0011473	HP:0011473	Villous atrophy	0	STX3 CL E G H	6809	11438	ORPHA:2290	Microvillus inclusion disease	HP:0040282 - Frequent	1
HP:0011473	HP:0011473	Villous atrophy	0	SYK CL E G H	6850	11491	OMIM:619381	IMMUNODEFICIENCY 82 WITH SYSTEMIC INFLAMMATION; IMD82		1
HP:0011473	HP:0011473	Villous atrophy	0	TOM1 CL E G H	10043	11982	ORPHA:391487	Autoimmune enteropathy and endocrinopathy-susceptibility to chronic infections syndrome	HP:0040282 - Frequent
HP:0011473	HP:0011473	Villous atrophy	0	TOM1 CL E G H	10043	11982	OMIM:619510	IMMUNODEFICIENCY 85 AND AUTOIMMUNITY; IMD85
HP:0011473	HP:0011473	Villous atrophy	0	UNC45A CL E G H	55898	30594	OMIM:619377	OSTEOOTOHEPATOENTERIC SYNDROME; OOHE
HP:0011473	HP:0011473	Villous atrophy	0	WNT2B CL E G H	7482	12781	OMIM:618168	Diarrhea 9		1

Genes (28) :ADAM17 ALG3 ALG9 CIITA DEF6 DGAT1 EPCAM FOXP3 IL2RA LRBA MPI MYO5B NLRC4 PCSK1 PERCC1 PMM2 RFX5 RFXANK RFXAP SKIC2 SKIC3 SPINK5 STAT1 STX3 SYK TOM1 UNC45A WNT2B

Diseases (29) :OMIM:614328 OMIM:601110 ORPHA:79328 OMIM:209920 OMIM:619573 OMIM:615863 ORPHA:92050 OMIM:613217 OMIM:304790 OMIM:606367 OMIM:614700 OMIM:602579 OMIM:251850 ORPHA:2290 OMIM:616050 OMIM:600955 OMIM:618662 OMIM:212065 ORPHA:84064 OMIM:614602 OMIM:222470 OMIM:256500 ORPHA:391487 OMIM:614162 OMIM:619445 OMIM:619381 OMIM:619510 OMIM:619377 OMIM:618168

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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