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:
Abnormal bone ossification (HP:0011849)

Grandparent Node:
Abnormality of skull ossification (HP:0002703)

Parent Node:
Abnormal calvaria morphology (HP:0002683)

Parent Node:
Decreased skull ossification (HP:0004331)

..Starting node
..Decreased calvarial ossification (HP:0005474)

Term ID:

5474

Name:

Decreased calvarial ossification

Synonym:

Poorly ossified calvaria; Poorly ossified calvarium; Skull soft on palpation; Soft calvaria; Soft skullcap; Undermineralized calvarium

Definition:

Abnormal reduction in ossification of the calvaria (roof of the skull consisting of the frontal bone, parietal bones, temporal bones, and occipital bone).

Comments:

Reference:

HP:0005474

Genes and Diseases:

Child Nodes:

........

Absent ossification of calvaria (HP:0005623)

Sister Nodes:

Decreased cranial base ossification (HP:0005451)

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:0005474	HP:0005474	Decreased calvarial ossification	0	ALPL CL E G H	249	438	OMIM:241500	Hypophosphatasia, infantile	.	126
HP:0005474	HP:0005474	Decreased calvarial ossification	0	COL1A1 CL E G H	1277	2197	OMIM:166210	Osteogenesis imperfecta, type IIA		373
HP:0005474	HP:0005474	Decreased calvarial ossification	0	COL1A1 CL E G H	1277	2197	OMIM:259420	Osteogenesis imperfecta, type III	.	373
HP:0005474	HP:0005474	Decreased calvarial ossification	0	COL1A2 CL E G H	1278	2198	OMIM:166210	Osteogenesis imperfecta, type IIA		243
HP:0005474	HP:0005474	Decreased calvarial ossification	0	COL1A2 CL E G H	1278	2198	OMIM:259420	Osteogenesis imperfecta, type III	.	243
HP:0005474	HP:0005474	Decreased calvarial ossification	0	CREB3L1 CL E G H	90993	18856	OMIM:616229	Osteogenesis imperfecta, type XVI		4
HP:0005474	HP:0005474	Decreased calvarial ossification	0	CRTAP CL E G H	10491	2379	OMIM:610682	Osteogenesis imperfecta, type VII	.	124
HP:0005474	HP:0005474	Decreased calvarial ossification	0	FGFR2 CL E G H	2263	3689	ORPHA:313855	FGFR2-related bent bone dysplasia	HP:0040281 - Very frequent	175
HP:0005474	HP:0005474	Decreased calvarial ossification	0	FIG4 CL E G H	9896	16873	OMIM:216340	Yunis-Varon syndrome		111
HP:0005474	HP:0005474	Decreased calvarial ossification	0	IFT43 CL E G H	112752	29669	OMIM:617866	SHORT-RIB THORACIC DYSPLASIA 18 WITH POLYDACTYLY; SRTD18		11
HP:0005474	HP:0005474	Decreased calvarial ossification	0	INTU CL E G H	27152	29239	OMIM:617925	Short-Rib thoracic dysplasia 20 with polydactyly
HP:0005474	HP:0005474	Decreased calvarial ossification	0	LAMA5 CL E G H	3911	6485	OMIM:620076			5
HP:0005474	HP:0005474	Decreased calvarial ossification	0	P3H1 CL E G H	64175	19316	OMIM:610915	Osteogenesis imperfecta, type VIII		43
HP:0005474	HP:0005474	Decreased calvarial ossification	0	PPIB CL E G H	5479	9255	OMIM:259440	Osteogenesis imperfecta, type IX		39
HP:0005474	HP:0005474	Decreased calvarial ossification	0	TXNDC15 CL E G H	79770	20652	OMIM:619879			2
HP:0005474	HP:0005474	Decreased calvarial ossification	0	WNT7A CL E G H	7476	12786	OMIM:276820	Ulna and fibula, absence of, with severe limb deficiency	.	13
HP:0005474	HP:0005474	Decreased calvarial ossification	0	ZMPSTE24 CL E G H	10269	12877	OMIM:275210	Restrictive dermopathy, lethal	.	83
HP:0005474	HP:0005623	Absent ossification of calvaria	1	COL1A1 CL E G H	1277	2197	OMIM:166210	Osteogenesis imperfecta, type IIA		373
HP:0005474	HP:0005623	Absent ossification of calvaria	1	COL1A2 CL E G H	1278	2198	OMIM:166210	Osteogenesis imperfecta, type IIA		243

Genes (15) :ALPL COL1A1 COL1A2 CREB3L1 CRTAP FGFR2 FIG4 IFT43 INTU LAMA5 P3H1 PPIB TXNDC15 WNT7A ZMPSTE24

Diseases (15) :OMIM:241500 OMIM:166210 OMIM:259420 OMIM:616229 OMIM:610682 ORPHA:313855 OMIM:216340 OMIM:617866 OMIM:617925 OMIM:620076 OMIM:610915 OMIM:259440 OMIM:619879 OMIM:276820 OMIM:275210

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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