Human Phenotype Ontology

About
MSeqDR-LSDB
Tools
- Quick-Mitome for WES
- Quick-Mitome
- Quick-Mitome Report
- mtDNA Tool:
- mvTool
- Phy-Mer
- MToolBox
- mvTool for Haplogroup
- mvTool with HmtDB
- MitoMaster
- MitoTIP tRNA Scoring
- MSeq-OpenCGA
- Variant Tool:
- VariantOneStop
- HBCR Exome (Retired)
- POLG Patho. Server
- Data - Awsomics GeEx
- Expert Panel
- Panel Tool:
- Gene Panel Examiner
- Transgenomic_NuclearMitome
- Pedigree Maker
- json2table
Phenome-Disease
Collaboration
- Genesis (GEM.App)
- LeighMap
- Expert Panel
- Collaboration Zone
Submission
- Submit_Interpret_Variant
- Instructions

Hello! Guest! Please Login or Register! Clinician Mode

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:
Abnormal renal medulla morphology (HP:0100957)

..Starting node
..Nephronophthisis (HP:0000090)

Term ID:

Name:

Nephronophthisis

Synonym:

juvenile nephronophthisis

Definition:

Presence of cysts at the corticomedullary junction of the kidney in combination with tubulointerstitial fibrosis.

Comments:

Reference:

HP:0000090

Genes and Diseases:

Child Nodes:

Sister Nodes:

Abnormal renal corticomedullary differentiation (HP:0005932)

Abnormality of medullary pyramid morphology (HP:0025361)

Multiple small medullary renal cysts (HP:0008659)

Renal corticomedullary cysts (HP:0000108)

Input	HPO ID	HPO term	Distance	Gene	Gene id entrez	HGNC ID	DiseaseId	DiseaseName	Frequency	Onset	ClinVar variants
HPO disease - gene - phenotype typical associations:
HPO disease - gene - phenotype less frequent non-typical associations:
HP:0000090	HP:0000090	Nephronophthisis	0	AHI1 CL E G H	54806	21575	OMIM:608629	Joubert syndrome 3	.		175
HP:0000090	HP:0000090	Nephronophthisis	0	ANKS6 CL E G H	203286	26724	OMIM:615382	Nephronophthisis 16	.		32
HP:0000090	HP:0000090	Nephronophthisis	0	CEP120 CL E G H	153241	26690	ORPHA:474	Jeune syndrome	HP:0040283 - Occasional		7
HP:0000090	HP:0000090	Nephronophthisis	0	CEP164 CL E G H	22897	29182	OMIM:614845	Nephronophthisis 15	.		34
HP:0000090	HP:0000090	Nephronophthisis	0	CEP164 CL E G H	22897	29182	ORPHA:3156	Senior-Loken syndrome	HP:0040282 - Frequent		34
HP:0000090	HP:0000090	Nephronophthisis	0	CEP290 CL E G H	80184	29021	OMIM:610188	Joubert syndrome 5	.		342
HP:0000090	HP:0000090	Nephronophthisis	0	CEP290 CL E G H	80184	29021	ORPHA:3156	Senior-Loken syndrome	HP:0040282 - Frequent		342
HP:0000090	HP:0000090	Nephronophthisis	0	CEP41 CL E G H	95681	12370	OMIM:614464	Joubert syndrome 15	HP:0040283 - Occasional		90
HP:0000090	HP:0000090	Nephronophthisis	0	CEP83 CL E G H	51134	17966	OMIM:615862	Nephronophthisis 18	.		10
HP:0000090	HP:0000090	Nephronophthisis	0	DCDC2 CL E G H	51473	18141	OMIM:616217	Nephronophthisis 19			8
HP:0000090	HP:0000090	Nephronophthisis	0	DYNC2H1 CL E G H	79659	2962	ORPHA:474	Jeune syndrome	HP:0040283 - Occasional		304
HP:0000090	HP:0000090	Nephronophthisis	0	DYNC2I1 CL E G H	55112	21862	ORPHA:474	Jeune syndrome	HP:0040283 - Occasional
HP:0000090	HP:0000090	Nephronophthisis	0	DYNC2I2 CL E G H	89891	28296	ORPHA:474	Jeune syndrome	HP:0040283 - Occasional
HP:0000090	HP:0000090	Nephronophthisis	0	DYNC2LI1 CL E G H	51626	24595	ORPHA:474	Jeune syndrome	HP:0040283 - Occasional		7
HP:0000090	HP:0000090	Nephronophthisis	0	FAN1 CL E G H	22909	29170	OMIM:614817	Interstitial nephritis, karyomegalic	.		15
HP:0000090	HP:0000090	Nephronophthisis	0	GLIS2 CL E G H	84662	29450	OMIM:611498	NEPHRONOPHTHISIS 7; NPHP7			83
HP:0000090	HP:0000090	Nephronophthisis	0	IFT140 CL E G H	9742	29077	ORPHA:474	Jeune syndrome	HP:0040283 - Occasional		148
HP:0000090	HP:0000090	Nephronophthisis	0	IFT140 CL E G H	9742	29077	OMIM:266920	Short-rib thoracic dysplasia 9 with or without polydactyly	.		148
HP:0000090	HP:0000090	Nephronophthisis	0	IFT172 CL E G H	26160	30391	ORPHA:474	Jeune syndrome	HP:0040283 - Occasional		48
HP:0000090	HP:0000090	Nephronophthisis	0	IFT172 CL E G H	26160	30391	OMIM:615630	Short-Rib thoracic dysplasia 10 with or without polydactyly	.		48
HP:0000090	HP:0000090	Nephronophthisis	0	IFT43 CL E G H	112752	29669	OMIM:614099	Cranioectodermal dysplasia 3	.		11
HP:0000090	HP:0000090	Nephronophthisis	0	IFT80 CL E G H	57560	29262	ORPHA:474	Jeune syndrome	HP:0040283 - Occasional		65
HP:0000090	HP:0000090	Nephronophthisis	0	INVS CL E G H	27130	17870	OMIM:602088	Nephronophthisis 2	.		106
HP:0000090	HP:0000090	Nephronophthisis	0	INVS CL E G H	27130	17870	ORPHA:3156	Senior-Loken syndrome	HP:0040282 - Frequent		106
HP:0000090	HP:0000090	Nephronophthisis	0	IQCB1 CL E G H	9657	28949	ORPHA:3156	Senior-Loken syndrome	HP:0040282 - Frequent		61
HP:0000090	HP:0000090	Nephronophthisis	0	IQCB1 CL E G H	9657	28949	OMIM:609254	Senior-Loken syndrome 5	.		61
HP:0000090	HP:0000090	Nephronophthisis	0	MAPKBP1 CL E G H	23005	29536	OMIM:617271	Nephronophthisis 20	.		6
HP:0000090	HP:0000090	Nephronophthisis	0	NEK8 CL E G H	284086	13387	OMIM:613824	NEPHRONOPHTHISIS 9; NPHP9			43
HP:0000090	HP:0000090	Nephronophthisis	0	NPHP1 CL E G H	4867	7905	OMIM:609583	Joubert syndrome 4	.		85
HP:0000090	HP:0000090	Nephronophthisis	0	NPHP1 CL E G H	4867	7905	OMIM:256100	Nephronophthisis 1			85
HP:0000090	HP:0000090	Nephronophthisis	0	NPHP1 CL E G H	4867	7905	ORPHA:3156	Senior-Loken syndrome	HP:0040282 - Frequent		85
HP:0000090	HP:0000090	Nephronophthisis	0	NPHP1 CL E G H	4867	7905	OMIM:266900	Senior-Loken syndrome 1	.	HP:0003621 - Juvenile onset	85
HP:0000090	HP:0000090	Nephronophthisis	0	NPHP3 CL E G H	27031	7907	OMIM:604387	Nephronophthisis 3	.		157
HP:0000090	HP:0000090	Nephronophthisis	0	NPHP3 CL E G H	27031	7907	ORPHA:3156	Senior-Loken syndrome	HP:0040282 - Frequent		157
HP:0000090	HP:0000090	Nephronophthisis	0	NPHP4 CL E G H	261734	19104	OMIM:606966	Nephronophthisis 4	.		220
HP:0000090	HP:0000090	Nephronophthisis	0	NPHP4 CL E G H	261734	19104	ORPHA:3156	Senior-Loken syndrome	HP:0040282 - Frequent		220
HP:0000090	HP:0000090	Nephronophthisis	0	NPHP4 CL E G H	261734	19104	OMIM:606996	Senior-Loken syndrome 4	.		220
HP:0000090	HP:0000090	Nephronophthisis	0	RPGRIP1L CL E G H	23322	29168	OMIM:619113	COACH SYNDROME 3; COACH3			167
HP:0000090	HP:0000090	Nephronophthisis	0	RPGRIP1L CL E G H	23322	29168	OMIM:611560	Joubert syndrome 7	.		167
HP:0000090	HP:0000090	Nephronophthisis	0	SDCCAG8 CL E G H	10806	10671	ORPHA:3156	Senior-Loken syndrome	HP:0040282 - Frequent		61
HP:0000090	HP:0000090	Nephronophthisis	0	SDCCAG8 CL E G H	10806	10671	OMIM:613615	SENIOR-LOKEN SYNDROME 7; SLSN7			61
HP:0000090	HP:0000090	Nephronophthisis	0	TMEM138 CL E G H	51524	26944	OMIM:614465	JOUBERT SYNDROME 16; JBTS16			39
HP:0000090	HP:0000090	Nephronophthisis	0	TMEM216 CL E G H	51259	25018	OMIM:608091	Joubert syndrome 2	.		45
HP:0000090	HP:0000090	Nephronophthisis	0	TMEM67 CL E G H	91147	28396	OMIM:216360	Coach syndrome 1			166
HP:0000090	HP:0000090	Nephronophthisis	0	TMEM67 CL E G H	91147	28396	OMIM:610688	Joubert syndrome 6	.		166
HP:0000090	HP:0000090	Nephronophthisis	0	TMEM67 CL E G H	91147	28396	OMIM:613550	NEPHRONOPHTHISIS 11; NPHP11			166
HP:0000090	HP:0000090	Nephronophthisis	0	TMEM67 CL E G H	91147	28396	OMIM:602152	Rhyns syndrome	.		166
HP:0000090	HP:0000090	Nephronophthisis	0	TMEM67 CL E G H	91147	28396	ORPHA:140976	RHYNS syndrome	HP:0040281 - Very frequent		166
HP:0000090	HP:0000090	Nephronophthisis	0	TRAF3IP1 CL E G H	26146	17861	ORPHA:3156	Senior-Loken syndrome	HP:0040282 - Frequent		6
HP:0000090	HP:0000090	Nephronophthisis	0	TRAF3IP1 CL E G H	26146	17861	OMIM:616629	Senior-Loken syndrome 9	.		6
HP:0000090	HP:0000090	Nephronophthisis	0	TRIP11 CL E G H	9321	12305	OMIM:184260	Osteochondrodysplasia			133
HP:0000090	HP:0000090	Nephronophthisis	0	TTC21B CL E G H	79809	25660	ORPHA:474	Jeune syndrome	HP:0040283 - Occasional		132
HP:0000090	HP:0000090	Nephronophthisis	0	TTC21B CL E G H	79809	25660	OMIM:613820	Nephronophthisis 12			132
HP:0000090	HP:0000090	Nephronophthisis	0	WDR19 CL E G H	57728	18340	ORPHA:474	Jeune syndrome	HP:0040283 - Occasional		95
HP:0000090	HP:0000090	Nephronophthisis	0	WDR19 CL E G H	57728	18340	OMIM:614377	Nephronophthisis 13	.		95
HP:0000090	HP:0000090	Nephronophthisis	0	WDR19 CL E G H	57728	18340	ORPHA:3156	Senior-Loken syndrome	HP:0040282 - Frequent		95
HP:0000090	HP:0000090	Nephronophthisis	0	WDR19 CL E G H	57728	18340	OMIM:616307	Senior-Loken syndrome 8	.		95
HP:0000090	HP:0000090	Nephronophthisis	0	XPNPEP3 CL E G H	63929	28052	OMIM:613159	Nephronophthisis-Like nephropathy 1	.		109
HP:0000090	HP:0000090	Nephronophthisis	0	ZNF423 CL E G H	23090	16762	OMIM:614844	Nephronophthisis 14	.		49

Genes (36) :AHI1 ANKS6 CEP120 CEP164 CEP290 CEP41 CEP83 DCDC2 DYNC2H1 DYNC2I1 DYNC2I2 DYNC2LI1 FAN1 GLIS2 IFT140 IFT172 IFT43 IFT80 INVS IQCB1 MAPKBP1 NEK8 NPHP1 NPHP3 NPHP4 RPGRIP1L SDCCAG8 TMEM138 TMEM216 TMEM67 TRAF3IP1 TRIP11 TTC21B WDR19 XPNPEP3 ZNF423

Diseases (41) :OMIM:608629 OMIM:615382 ORPHA:474 OMIM:614845 ORPHA:3156 OMIM:610188 OMIM:614464 OMIM:615862 OMIM:616217 OMIM:614817 OMIM:611498 OMIM:266920 OMIM:615630 OMIM:614099 OMIM:602088 OMIM:609254 OMIM:617271 OMIM:613824 OMIM:609583 OMIM:256100 OMIM:266900 OMIM:604387 OMIM:606966 OMIM:606996 OMIM:619113 OMIM:611560 OMIM:613615 OMIM:614465 OMIM:608091 OMIM:216360 OMIM:610688 OMIM:613550 OMIM:602152 ORPHA:140976 OMIM:616629 OMIM:184260 OMIM:613820 OMIM:614377 OMIM:616307 OMIM:613159 OMIM:614844

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

Feedback about the webpages , or email to MSeqDR webmaster: Lishuang Shen