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 skull morphology (HP:0000929)

Parent Node:
Abnormal calvaria morphology (HP:0002683)

..Starting node
..Thickened calvaria (HP:0002684)

Term ID:

2684

Name:

Thickened calvaria

Synonym:

Calvarial thickening; Calvarium thickened; Increased calvarial thickness; Increased thickness of calvaria; Increased thickness of calvarium; Increased thickness of cranial vault; Increased thickness of cranium; Increased thickness of skull cap; Thick calvaria; Thick calvarium; Thickened calvarium; Thickened cranial vault; Thickened cranium; Thickened skull cap; Thickening of the calvaria

Definition:

The presence of an abnormally thick calvaria.

Comments:

Reference:

HP:0002684

Genes and Diseases:

Child Nodes:

Sister Nodes:

Abnormality of the fontanelles or cranial sutures (HP:0000235)

Cranial hyperostosis (HP:0004437)

Decreased calvarial ossification (HP:0005474)

Dense calvaria (HP:0000250)

obsolete Abnormality of calvarial morphology (HP:0002648)

Thin calvarium (HP:0010539)

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:0002684	HP:0002684	Thickened calvaria	0	AGA CL E G H	175	318	ORPHA:93	Aspartylglucosaminuria	HP:0040282 - Frequent	76
HP:0002684	HP:0002684	Thickened calvaria	0	AGA CL E G H	175	318	OMIM:208400	ASPARTYLGLUCOSAMINURIA	.	76
HP:0002684	HP:0002684	Thickened calvaria	0	AMER1 CL E G H	139285	26837	OMIM:300373	Osteopathia striata with cranial sclerosis	.	34
HP:0002684	HP:0002684	Thickened calvaria	0	AMER1 CL E G H	139285	26837	ORPHA:2780	Osteopathia striata-cranial sclerosis syndrome	HP:0040281 - Very frequent	34
HP:0002684	HP:0002684	Thickened calvaria	0	AP1S2 CL E G H	8905	560	ORPHA:85335	Fried syndrome	HP:0040283 - Occasional	13
HP:0002684	HP:0002684	Thickened calvaria	0	CA2 CL E G H	760	1373	ORPHA:2785	Osteopetrosis with renal tubular acidosis		29
HP:0002684	HP:0002684	Thickened calvaria	0	CDH11 CL E G H	1009	1750	ORPHA:1299	Branchioskeletogenital syndrome	HP:0040281 - Very frequent	2
HP:0002684	HP:0002684	Thickened calvaria	0	COL11A1 CL E G H	1301	2186	ORPHA:560	Marshall syndrome	HP:0040282 - Frequent	215
HP:0002684	HP:0002684	Thickened calvaria	0	COL11A1 CL E G H	1301	2186	OMIM:154780	Marshall syndrome	.	215
HP:0002684	HP:0002684	Thickened calvaria	0	CSF3R CL E G H	1441	2439	OMIM:162830	Neutrophilia, hereditary	.	34
HP:0002684	HP:0002684	Thickened calvaria	0	DVL1 CL E G H	1855	3084	OMIM:616331	Robinow syndrome, autosomal dominant 2		14
HP:0002684	HP:0002684	Thickened calvaria	0	DYM CL E G H	54808	21317	OMIM:223800	Dyggve-Melchior-Clausen disease	.	65
HP:0002684	HP:0002684	Thickened calvaria	0	ERCC6 CL E G H	2074	3438	OMIM:133540	Cockayne syndrome, type B	.	199
HP:0002684	HP:0002684	Thickened calvaria	0	ERCC8 CL E G H	1161	3439	OMIM:216400	Cockayne syndrome A	.	55
HP:0002684	HP:0002684	Thickened calvaria	0	FLNA CL E G H	2316	3754	ORPHA:90650	Otopalatodigital syndrome type 1	HP:0040282 - Frequent	493
HP:0002684	HP:0002684	Thickened calvaria	0	FLNA CL E G H	2316	3754	ORPHA:90652	Otopalatodigital syndrome type 2	HP:0040282 - Frequent	493
HP:0002684	HP:0002684	Thickened calvaria	0	GLB1 CL E G H	2720	4298	ORPHA:79255	GM1 gangliosidosis type 1	HP:0040283 - Occasional	120
HP:0002684	HP:0002684	Thickened calvaria	0	GNAS CL E G H	2778	4392	ORPHA:79443	Pseudohypoparathyroidism type 1A	HP:0040282 - Frequent	101
HP:0002684	HP:0002684	Thickened calvaria	0	GNAS CL E G H	2778	4392	OMIM:103580	Pseudohypoparathyroidism, type IA	.	101
HP:0002684	HP:0002684	Thickened calvaria	0	GNPTAB CL E G H	79158	29670	OMIM:252500	Mucolipidosis II alpha/beta	.	240
HP:0002684	HP:0002684	Thickened calvaria	0	HPGD CL E G H	3248	5154	OMIM:259100	Hypertrophic osteoarthropathy, primary, autosomal recessive 1	.	55
HP:0002684	HP:0002684	Thickened calvaria	0	IFIH1 CL E G H	64135	18873	OMIM:182250	Singleton-Merten syndrome 1		28
HP:0002684	HP:0002684	Thickened calvaria	0	LRP5 CL E G H	4041	6697	OMIM:607634	Osteopetrosis, autosomal dominant 1	.	125
HP:0002684	HP:0002684	Thickened calvaria	0	LRP5 CL E G H	4041	6697	ORPHA:178377	Osteosclerosis-developmental delay-craniosynostosis syndrome	HP:0040281 - Very frequent	125
HP:0002684	HP:0002684	Thickened calvaria	0	MAN2B1 CL E G H	4125	6826	OMIM:248500	Alpha-mannosidosis	.	136
HP:0002684	HP:0002684	Thickened calvaria	0	MAN2B1 CL E G H	4125	6826	ORPHA:309282	Alpha-mannosidosis, infantile form	HP:0040283 - Occasional	136
HP:0002684	HP:0002684	Thickened calvaria	0	NONO CL E G H	4841	7871	ORPHA:466791	Macrocephaly-intellectual disability-left ventricular non compaction syndrome	HP:0040283 - Occasional	10
HP:0002684	HP:0002684	Thickened calvaria	0	NONO CL E G H	4841	7871	OMIM:300967	MENTAL RETARDATION, X-LINKED, SYNDROMIC 34; MRXS34		10
HP:0002684	HP:0002684	Thickened calvaria	0	PDE4D CL E G H	5144	8783	ORPHA:439822	PDE4D haploinsufficiency syndrome	HP:0040283 - Occasional	113
HP:0002684	HP:0002684	Thickened calvaria	0	PHF6 CL E G H	84295	18145	OMIM:301900	Borjeson-Forssman-Lehmann syndrome	.	29
HP:0002684	HP:0002684	Thickened calvaria	0	PLEKHM1 CL E G H	9842	29017	OMIM:618107	OSTEOPETROSIS, AUTOSOMAL DOMINANT 3; OPTA3		2
HP:0002684	HP:0002684	Thickened calvaria	0	POLR3A CL E G H	11128	30074	ORPHA:3455	Wiedemann-Rautenstrauch syndrome	HP:0040282 - Frequent	138
HP:0002684	HP:0002684	Thickened calvaria	0	PTDSS1 CL E G H	9791	9587	ORPHA:2658	Lenz-Majewski hyperostotic dwarfism	HP:0040281 - Very frequent	6
HP:0002684	HP:0002684	Thickened calvaria	0	PTH1R CL E G H	5745	9608	OMIM:600002	Eiken syndrome		58
HP:0002684	HP:0002684	Thickened calvaria	0	RPS6KA3 CL E G H	6197	10432	OMIM:303600	Coffin-Lowry syndrome	.	65
HP:0002684	HP:0002684	Thickened calvaria	0	RUNX2 CL E G H	860	10472	OMIM:119600	Cleidocranial dysplasia	.	90
HP:0002684	HP:0002684	Thickened calvaria	0	SFRP4 CL E G H	6424	10778	OMIM:265900	Pyle disease	.	3
HP:0002684	HP:0002684	Thickened calvaria	0	SGMS2 CL E G H	166929	28395	OMIM:126550	Calvarial doughnut lesions with bone fragility	.
HP:0002684	HP:0002684	Thickened calvaria	0	SLC17A5 CL E G H	26503	10933	OMIM:604369	Salla disease	.	78
HP:0002684	HP:0002684	Thickened calvaria	0	SMAD4 CL E G H	4089	6770	OMIM:139210	Myhre syndrome		504
HP:0002684	HP:0002684	Thickened calvaria	0	SMS CL E G H	6611	11123	OMIM:309583	Mental retardation, X-linked, syndromic, Snyder-Robinson type		19
HP:0002684	HP:0002684	Thickened calvaria	0	SNX14 CL E G H	57231	14977	ORPHA:397709	Intellectual disability-coarse face-macrocephaly-cerebellar hypotrophy syndrome	HP:0040283 - Occasional	14
HP:0002684	HP:0002684	Thickened calvaria	0	TMEM53 CL E G H	79639	26186	OMIM:619727	CRANIOTUBULAR DYSPLASIA, IKEGAWA TYPE; CTDI
HP:0002684	HP:0002684	Thickened calvaria	0	TMEM67 CL E G H	91147	28396	OMIM:602152	Rhyns syndrome	.	166
HP:0002684	HP:0002684	Thickened calvaria	0	TNFRSF11B CL E G H	4982	11909	OMIM:239000	Paget disease of bone 5, juvenile-onset	.	44

Genes (37) :AGA AMER1 AP1S2 CA2 CDH11 COL11A1 CSF3R DVL1 DYM ERCC6 ERCC8 FLNA GLB1 GNAS GNPTAB HPGD IFIH1 LRP5 MAN2B1 NONO PDE4D PHF6 PLEKHM1 POLR3A PTDSS1 PTH1R RPS6KA3 RUNX2 SFRP4 SGMS2 SLC17A5 SMAD4 SMS SNX14 TMEM53 TMEM67 TNFRSF11B

Diseases (45) :ORPHA:93 OMIM:208400 OMIM:300373 ORPHA:2780 ORPHA:85335 ORPHA:2785 ORPHA:1299 ORPHA:560 OMIM:154780 OMIM:162830 OMIM:616331 OMIM:223800 OMIM:133540 OMIM:216400 ORPHA:90650 ORPHA:90652 ORPHA:79255 ORPHA:79443 OMIM:103580 OMIM:252500 OMIM:259100 OMIM:182250 OMIM:607634 ORPHA:178377 OMIM:248500 ORPHA:309282 ORPHA:466791 OMIM:300967 ORPHA:439822 OMIM:301900 OMIM:618107 ORPHA:3455 ORPHA:2658 OMIM:600002 OMIM:303600 OMIM:119600 OMIM:265900 OMIM:126550 OMIM:604369 OMIM:139210 OMIM:309583 ORPHA:397709 OMIM:619727 OMIM:602152 OMIM:239000

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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