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 bone mineral density (HP:0004348)

Parent Node:
Reduced bone mineral density (HP:0004349)

..Starting node
..Osteomalacia (HP:0002749)

Term ID:

2749

Name:

Osteomalacia

Synonym:

Softening of the bones

Definition:

Osteomalacia is a general term for bone weakness owing to a defect in mineralization of the protein framework known as osteoid. This defective mineralization is mainly caused by lack in vitamin D. Osteomalacia in children is known as rickets.

Comments:

Reference:

HP:0002749

Genes and Diseases:

Child Nodes:

Sister Nodes:

Generalized bone demineralization (HP:0006462)

Osteopenia (HP:0000938)

Osteoporosis (HP:0000939)

Patchy reduction of bone mineral density (HP:0010657)

Patchy variation in bone mineral density (HP:0010659)

Rickets (HP:0002748)

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:0002749	HP:0002749	Osteomalacia	0	ABCC6 CL E G H	368	57	ORPHA:51608	Generalized arterial calcification of infancy	HP:0040282 - Frequent	415
HP:0002749	HP:0002749	Osteomalacia	0	ADAMTS2 CL E G H	9509	218	ORPHA:1901	Dermatosparaxis Ehlers-Danlos syndrome	HP:0040281 - Very frequent	165
HP:0002749	HP:0002749	Osteomalacia	0	ADAMTSL2 CL E G H	9719	14631	ORPHA:1901	Dermatosparaxis Ehlers-Danlos syndrome	HP:0040281 - Very frequent	72
HP:0002749	HP:0002749	Osteomalacia	0	ALPL CL E G H	249	438	OMIM:146300	Hypophosphatasia, adult	.	126
HP:0002749	HP:0002749	Osteomalacia	0	ANTXR2 CL E G H	118429	21732	ORPHA:2176	Infantile systemic hyalinosis	HP:0040281 - Very frequent	49
HP:0002749	HP:0002749	Osteomalacia	0	AP2S1 CL E G H	1175	565	OMIM:600740	Hypocalciuric hypercalcemia, familial, type III	.	6
HP:0002749	HP:0002749	Osteomalacia	0	ATP7A CL E G H	538	869	ORPHA:198	Occipital horn syndrome	HP:0040282 - Frequent	192
HP:0002749	HP:0002749	Osteomalacia	0	ATP7B CL E G H	540	870	OMIM:277900	Wilson disease	.	315
HP:0002749	HP:0002749	Osteomalacia	0	CLCN5 CL E G H	1184	2023	OMIM:300009	Dent disease 1	.	112
HP:0002749	HP:0002749	Osteomalacia	0	CLCN5 CL E G H	1184	2023	OMIM:300554	Hypophosphatemic rickets, X-linked recessive	.	112
HP:0002749	HP:0002749	Osteomalacia	0	CYP27B1 CL E G H	1594	2606	ORPHA:289157	Hypocalcemic vitamin D-dependent rickets	HP:0040281 - Very frequent	41
HP:0002749	HP:0002749	Osteomalacia	0	CYP2R1 CL E G H	120227	20580	ORPHA:289157	Hypocalcemic vitamin D-dependent rickets	HP:0040281 - Very frequent	5
HP:0002749	HP:0002749	Osteomalacia	0	DMP1 CL E G H	1758	2932	ORPHA:289176	Autosomal recessive hypophosphatemic rickets	HP:0040281 - Very frequent	48
HP:0002749	HP:0002749	Osteomalacia	0	EHHADH CL E G H	1962	3247	ORPHA:3337	Primary Fanconi renotubular syndrome	HP:0040282 - Frequent	2
HP:0002749	HP:0002749	Osteomalacia	0	ENPP1 CL E G H	5167	3356	ORPHA:289176	Autosomal recessive hypophosphatemic rickets	HP:0040281 - Very frequent	151
HP:0002749	HP:0002749	Osteomalacia	0	ENPP1 CL E G H	5167	3356	ORPHA:51608	Generalized arterial calcification of infancy	HP:0040282 - Frequent	151
HP:0002749	HP:0002749	Osteomalacia	0	FGF23 CL E G H	8074	3680	ORPHA:89937	Autosomal dominant hypophosphatemic rickets	HP:0040282 - Frequent	51
HP:0002749	HP:0002749	Osteomalacia	0	FGF23 CL E G H	8074	3680	OMIM:193100	Hypophosphatemic rickets, autosomal dominant	.	51
HP:0002749	HP:0002749	Osteomalacia	0	GATM CL E G H	2628	4175	OMIM:134600	Fanconi renotubular syndrome 1	.	86
HP:0002749	HP:0002749	Osteomalacia	0	GATM CL E G H	2628	4175	ORPHA:3337	Primary Fanconi renotubular syndrome	HP:0040282 - Frequent	86
HP:0002749	HP:0002749	Osteomalacia	0	GNAS CL E G H	2778	4392	ORPHA:562	McCune-Albright syndrome	HP:0040283 - Occasional	101
HP:0002749	HP:0002749	Osteomalacia	0	NDUFAF6 CL E G H	137682	28625	ORPHA:3337	Primary Fanconi renotubular syndrome	HP:0040282 - Frequent	39
HP:0002749	HP:0002749	Osteomalacia	0	OCRL CL E G H	4952	8108	OMIM:309000	Lowe syndrome	.	88
HP:0002749	HP:0002749	Osteomalacia	0	OCRL CL E G H	4952	8108	ORPHA:534	Oculocerebrorenal syndrome of Lowe	HP:0040282 - Frequent	88
HP:0002749	HP:0002749	Osteomalacia	0	PHEX CL E G H	5251	8918	OMIM:307800	Hypophosphatemic rickets, X-linked dominant	.	217
HP:0002749	HP:0002749	Osteomalacia	0	RNU4ATAC CL E G H	100151683	34016	ORPHA:2636	Microcephalic osteodysplastic primordial dwarfism types I and III	HP:0040281 - Very frequent	15
HP:0002749	HP:0002749	Osteomalacia	0	SLC2A2 CL E G H	6514	11006	OMIM:227810	Fanconi-Bickel syndrome	.	71
HP:0002749	HP:0002749	Osteomalacia	0	SLC34A1 CL E G H	6569	11019	ORPHA:157215	Hereditary hypophosphatemic rickets with hypercalciuria	HP:0040282 - Frequent	47
HP:0002749	HP:0002749	Osteomalacia	0	SLC34A1 CL E G H	6569	11019	ORPHA:3337	Primary Fanconi renotubular syndrome	HP:0040282 - Frequent	47
HP:0002749	HP:0002749	Osteomalacia	0	SLC34A3 CL E G H	142680	20305	ORPHA:157215	Hereditary hypophosphatemic rickets with hypercalciuria	HP:0040282 - Frequent	52
HP:0002749	HP:0002749	Osteomalacia	0	SLC4A1 CL E G H	6521	11027	OMIM:179800	Renal tubular acidosis, distal, autosomal dominant	.	109
HP:0002749	HP:0002749	Osteomalacia	0	SYK CL E G H	6850	11491	OMIM:619381	IMMUNODEFICIENCY 82 WITH SYSTEMIC INFLAMMATION; IMD82		1
HP:0002749	HP:0002749	Osteomalacia	0	VDR CL E G H	7421	12679	ORPHA:93160	Hypocalcemic vitamin D-resistant rickets	HP:0040281 - Very frequent	104

Genes (27) :ABCC6 ADAMTS2 ADAMTSL2 ALPL ANTXR2 AP2S1 ATP7A ATP7B CLCN5 CYP27B1 CYP2R1 DMP1 EHHADH ENPP1 FGF23 GATM GNAS NDUFAF6 OCRL PHEX RNU4ATAC SLC2A2 SLC34A1 SLC34A3 SLC4A1 SYK VDR

Diseases (25) :ORPHA:51608 ORPHA:1901 OMIM:146300 ORPHA:2176 OMIM:600740 ORPHA:198 OMIM:277900 OMIM:300009 OMIM:300554 ORPHA:289157 ORPHA:289176 ORPHA:3337 ORPHA:89937 OMIM:193100 OMIM:134600 ORPHA:562 OMIM:309000 ORPHA:534 OMIM:307800 ORPHA:2636 OMIM:227810 ORPHA:157215 OMIM:179800 OMIM:619381 ORPHA:93160

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