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:
Abnormality of lipoprotein cholesterol concentration (HP:0010979)

Parent Node:
Abnormal HDL cholesterol concentration (HP:0031888)

Parent Node:
Hypolipoproteinemia (HP:0010981)

..Starting node
..Decreased HDL cholesterol concentration (HP:0003233)

Term ID:

3233

Name:

Decreased HDL cholesterol concentration

Synonym:

Decreased circulating high-density lipoprotein cholesterol; Decreased circulating high-density lipoprotein levels; Decreased HDL cholesterol; Hypoalphalipoproteinemia; Low HDL-cholesterol

Definition:

An decreased concentration of high-density lipoprotein cholesterol in the blood.

Comments:

Reference:

HP:0003233

Genes and Diseases:

Child Nodes:

Sister Nodes:

Decreased circulating chylomicron concentration (HP:0031242)

Decreased LDL cholesterol concentration (HP:0003563)

Decreased VLDL cholesterol concentration (HP:0031243)

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:0003233	HP:0003233	Decreased HDL cholesterol concentration	0	ABCA1 CL E G H	19	29	ORPHA:425	Apolipoprotein A-I deficiency	HP:0040282 - Frequent	191
HP:0003233	HP:0003233	Decreased HDL cholesterol concentration	0	ABCA1 CL E G H	19	29	OMIM:604091	HYPOALPHALIPOPROTEINEMIA, PRIMARY		191
HP:0003233	HP:0003233	Decreased HDL cholesterol concentration	0	ABCA1 CL E G H	19	29	OMIM:205400	Tangier disease	.	191
HP:0003233	HP:0003233	Decreased HDL cholesterol concentration	0	ALMS1 CL E G H	7840	428	OMIM:203800	Alstrom syndrome	.	404
HP:0003233	HP:0003233	Decreased HDL cholesterol concentration	0	APOA1 CL E G H	335	600	ORPHA:425	Apolipoprotein A-I deficiency	HP:0040282 - Frequent	40
HP:0003233	HP:0003233	Decreased HDL cholesterol concentration	0	APOA1 CL E G H	335	600	OMIM:618463	HYPOALPHALIPOPROTEINEMIA, PRIMARY, 2		40
HP:0003233	HP:0003233	Decreased HDL cholesterol concentration	0	APOA1 CL E G H	335	600	OMIM:619836	HYPOALPHALIPOPROTEINEMIA, PRIMARY, 2, INTERMEDIATE		40
HP:0003233	HP:0003233	Decreased HDL cholesterol concentration	0	APOA5 CL E G H	116519	17288	OMIM:144650	Hyperlipoproteinemia, type V	.	7
HP:0003233	HP:0003233	Decreased HDL cholesterol concentration	0	APOB CL E G H	338	603	OMIM:615558	Hypobetalipoproteinemia, familial, 1		356
HP:0003233	HP:0003233	Decreased HDL cholesterol concentration	0	APOE CL E G H	348	613	ORPHA:412	Dysbetalipoproteinemia	HP:0040281 - Very frequent	39
HP:0003233	HP:0003233	Decreased HDL cholesterol concentration	0	CELA2A CL E G H	63036	24609	OMIM:618620	ABDOMINAL OBESITY-METABOLIC SYNDROME 4; AOMS4		1
HP:0003233	HP:0003233	Decreased HDL cholesterol concentration	0	CEP19 CL E G H	84984	28209	OMIM:615703	Morbid obesity and spermatogenic failure		1
HP:0003233	HP:0003233	Decreased HDL cholesterol concentration	0	CREB3L3 CL E G H	84699	18855	OMIM:619324	HYPERTRIGLYCERIDEMIA 2; HYTG2
HP:0003233	HP:0003233	Decreased HDL cholesterol concentration	0	GALNT2 CL E G H	2590	4124	OMIM:618885	CONGENITAL DISORDER OF GLYCOSYLATION, TYPE IIt; CDG2T
HP:0003233	HP:0003233	Decreased HDL cholesterol concentration	0	GPIHBP1 CL E G H	338328	24945	OMIM:615947	Hyperlipoproteinemia, type ID		12
HP:0003233	HP:0003233	Decreased HDL cholesterol concentration	0	LCAT CL E G H	3931	6522	ORPHA:79292	Fish-eye disease	HP:0040281 - Very frequent	26
HP:0003233	HP:0003233	Decreased HDL cholesterol concentration	0	LCAT CL E G H	3931	6522	OMIM:136120	Fish-Eye disease	.	26
HP:0003233	HP:0003233	Decreased HDL cholesterol concentration	0	LCAT CL E G H	3931	6522	OMIM:245900	Lecithin:cholesterol acyltransferase deficiency	.	26
HP:0003233	HP:0003233	Decreased HDL cholesterol concentration	0	LIPA CL E G H	3988	6617	OMIM:278000	Lysosomal acid lipase deficiency		73
HP:0003233	HP:0003233	Decreased HDL cholesterol concentration	0	LMNA CL E G H	4000	6636	ORPHA:280365	Autosomal semi-dominant severe lipodystrophic laminopathy	HP:0040282 - Frequent	645
HP:0003233	HP:0003233	Decreased HDL cholesterol concentration	0	LMNA CL E G H	4000	6636	OMIM:151660	Lipodystrophy, familial partial, type 2	.	645
HP:0003233	HP:0003233	Decreased HDL cholesterol concentration	0	MSMO1 CL E G H	6307	10545	OMIM:616834	Microcephaly, congenital cataract, and psoriasiform dermatitis		3
HP:0003233	HP:0003233	Decreased HDL cholesterol concentration	0	MTTP CL E G H	4547	7467	ORPHA:14	Abetalipoproteinemia	HP:0040282 - Frequent	81
HP:0003233	HP:0003233	Decreased HDL cholesterol concentration	0	PPARG CL E G H	5468	9236	OMIM:604367	Lipodystrophy, familial partial, type 3	.	42
HP:0003233	HP:0003233	Decreased HDL cholesterol concentration	0	PSMB8 CL E G H	5696	9545	OMIM:256040	Proteasome-associated autoinflammatory syndrome 1 and digenic forms		20
HP:0003233	HP:0003233	Decreased HDL cholesterol concentration	0	SLC25A13 CL E G H	10165	10983	ORPHA:247585	Citrullinemia type II	HP:0040283 - Occasional	82
HP:0003233	HP:0003233	Decreased HDL cholesterol concentration	0	SLC25A13 CL E G H	10165	10983	OMIM:605814	Citrullinemia, type II, neonatal-onset	.	82
HP:0003233	HP:0003233	Decreased HDL cholesterol concentration	0	SLC25A13 CL E G H	10165	10983	ORPHA:247598	Neonatal intrahepatic cholestasis due to citrin deficiency	HP:0040283 - Occasional	82
HP:0003233	HP:0003233	Decreased HDL cholesterol concentration	0	SLC7A7 CL E G H	9056	11065	ORPHA:470	Lysinuric protein intolerance	HP:0040282 - Frequent	104
HP:0003233	HP:0003233	Decreased HDL cholesterol concentration	0	SMPD1 CL E G H	6609	11120	ORPHA:77293	Niemann-Pick disease type B	HP:0040282 - Frequent	164
HP:0003233	HP:0003233	Decreased HDL cholesterol concentration	0	SMPD1 CL E G H	6609	11120	OMIM:607616	Niemann-pick disease, type B	.	164

Genes (21) :ABCA1 ALMS1 APOA1 APOA5 APOB APOE CELA2A CEP19 CREB3L3 GALNT2 GPIHBP1 LCAT LIPA LMNA MSMO1 MTTP PPARG PSMB8 SLC25A13 SLC7A7 SMPD1

Diseases (30) :ORPHA:425 OMIM:604091 OMIM:205400 OMIM:203800 OMIM:618463 OMIM:619836 OMIM:144650 OMIM:615558 ORPHA:412 OMIM:618620 OMIM:615703 OMIM:619324 OMIM:618885 OMIM:615947 ORPHA:79292 OMIM:136120 OMIM:245900 OMIM:278000 ORPHA:280365 OMIM:151660 OMIM:616834 ORPHA:14 OMIM:604367 OMIM:256040 ORPHA:247585 OMIM:605814 ORPHA:247598 ORPHA:470 ORPHA:77293 OMIM:607616

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