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 form of the vertebral bodies (HP:0003312)

Parent Node:
Abnormality of the vertebral endplates (HP:0005106)

..Starting node
..Irregular vertebral endplates (HP:0003301)

Term ID:

3301

Name:

Irregular vertebral endplates

Synonym:

end-plate irregularities; endplate irregularities; endplate irregularity; Irregular end plates; Irregular endplates; irregular vertebral plates; vertebral endplate irregularity

Definition:

An irregular surface of the vertebral end plates, which are normally relatively smooth.

Comments:

Reference:

HP:0003301

Genes and Diseases:

Child Nodes:

........

Hump-shaped mound of bone in central and posterior portions of vertebral endplate (HP:0004594)

........

Irregular sclerotic endplates (HP:0008476)

Sister Nodes:

Hyperconvex vertebral body endplates (HP:0004603)

Sclerotic vertebral endplates (HP:0004576)

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:0003301	HP:0003301	Irregular vertebral endplates	0	ACP5 CL E G H	54	124	OMIM:607944	Spondyloenchondrodysplasia with immune dysregulation	.	16
HP:0003301	HP:0003301	Irregular vertebral endplates	0	B3GALT6 CL E G H	126792	17978	OMIM:271640	Spondyloepimetaphyseal dysplasia with joint laxity, type 1, with or without fractures	.	38
HP:0003301	HP:0003301	Irregular vertebral endplates	0	CCN6 CL E G H	8838	12771	ORPHA:1159	Progressive pseudorheumatoid arthropathy of childhood	HP:0040281 - Very frequent
HP:0003301	HP:0003301	Irregular vertebral endplates	0	CHST3 CL E G H	9469	1971	OMIM:143095	Spondyloepiphyseal dysplasia with congenital joint dislocations	.	165
HP:0003301	HP:0003301	Irregular vertebral endplates	0	COL10A1 CL E G H	1300	2185	ORPHA:174	Metaphyseal chondrodysplasia, Schmid type	HP:0040283 - Occasional	79
HP:0003301	HP:0003301	Irregular vertebral endplates	0	COL10A1 CL E G H	1300	2185	OMIM:156500	Metaphyseal chondrodysplasia, Schmid type	.	79
HP:0003301	HP:0003301	Irregular vertebral endplates	0	COL11A1 CL E G H	1301	2186	ORPHA:250984	Autosomal recessive Stickler syndrome	HP:0040282 - Frequent	215
HP:0003301	HP:0003301	Irregular vertebral endplates	0	COL2A1 CL E G H	1280	2200	OMIM:609162	Czech dysplasia, Metatarsal type	.	284
HP:0003301	HP:0003301	Irregular vertebral endplates	0	COL2A1 CL E G H	1280	2200	OMIM:604864	Osteoarthritis with mild chondrodysplasia	.	284
HP:0003301	HP:0003301	Irregular vertebral endplates	0	COL9A1 CL E G H	1297	2217	ORPHA:250984	Autosomal recessive Stickler syndrome	HP:0040282 - Frequent	110
HP:0003301	HP:0003301	Irregular vertebral endplates	0	COL9A1 CL E G H	1297	2217	OMIM:614135	Epiphyseal dysplasia, multiple, 6		110
HP:0003301	HP:0003301	Irregular vertebral endplates	0	COL9A2 CL E G H	1298	2218	ORPHA:250984	Autosomal recessive Stickler syndrome	HP:0040282 - Frequent	110
HP:0003301	HP:0003301	Irregular vertebral endplates	0	COL9A3 CL E G H	1299	2219	ORPHA:250984	Autosomal recessive Stickler syndrome	HP:0040282 - Frequent	137
HP:0003301	HP:0003301	Irregular vertebral endplates	0	COMP CL E G H	1311	2227	OMIM:132400	Epiphyseal dysplasia, multiple, 1	.	89
HP:0003301	HP:0003301	Irregular vertebral endplates	0	EIF2AK3 CL E G H	9451	3255	OMIM:226980	Epiphyseal dysplasia, multiple, with early-onset diabetes mellitus	.	65
HP:0003301	HP:0003301	Irregular vertebral endplates	0	EXOC6B CL E G H	23233	17085	OMIM:618395	Spondyloepimetaphyseal dysplasia with joint laxity, type 3	.	3
HP:0003301	HP:0003301	Irregular vertebral endplates	0	GNPAT CL E G H	8443	4416	OMIM:222765	Rhizomelic chondrodysplasia punctata, type 2	.	58
HP:0003301	HP:0003301	Irregular vertebral endplates	0	GORAB CL E G H	92344	25676	OMIM:231070	Geroderma osteodysplasticum	.	52
HP:0003301	HP:0003301	Irregular vertebral endplates	0	IDH1 CL E G H	3417	5382	ORPHA:99646	Metaphyseal chondromatosis with D-2-hydroxyglutaric aciduria		15
HP:0003301	HP:0003301	Irregular vertebral endplates	0	KIF22 CL E G H	3835	6391	OMIM:603546	Spondyloepimetaphyseal dysplasia with joint laxity, type 2	.	14
HP:0003301	HP:0003301	Irregular vertebral endplates	0	LOXL3 CL E G H	84695	13869	ORPHA:250984	Autosomal recessive Stickler syndrome	HP:0040282 - Frequent	4
HP:0003301	HP:0003301	Irregular vertebral endplates	0	MMP13 CL E G H	4322	7159	OMIM:602111	Spondyloepimetaphyseal dysplasia, Missouri type		52
HP:0003301	HP:0003301	Irregular vertebral endplates	0	NANS CL E G H	54187	19237	OMIM:610442	Spondyloepimetaphyseal dysplasia, Genevieve type	.	8
HP:0003301	HP:0003301	Irregular vertebral endplates	0	PAPSS2 CL E G H	9060	8604	OMIM:612847	Brachyolmia 4 with mild epiphyseal and metaphyseal changes	.	20
HP:0003301	HP:0003301	Irregular vertebral endplates	0	PDE4D CL E G H	5144	8783	ORPHA:439822	PDE4D haploinsufficiency syndrome	HP:0040283 - Occasional	113
HP:0003301	HP:0003301	Irregular vertebral endplates	0	POLR3A CL E G H	11128	30074	ORPHA:3455	Wiedemann-Rautenstrauch syndrome		138
HP:0003301	HP:0003301	Irregular vertebral endplates	0	RNU4ATAC CL E G H	100151683	34016	OMIM:616651	Roifman syndrome	.	15
HP:0003301	HP:0003301	Irregular vertebral endplates	0	SLC10A7 CL E G H	84068	23088	OMIM:618363	Short stature, amelogenesis imperfecta, and skeletal dysplasia with scoliosis	.
HP:0003301	HP:0003301	Irregular vertebral endplates	0	SLC29A3 CL E G H	55315	23096	ORPHA:1782	Dysosteosclerosis	HP:0040281 - Very frequent	68
HP:0003301	HP:0003301	Irregular vertebral endplates	0	SLC39A13 CL E G H	91252	20859	OMIM:612350	Ehlers-Danlos syndrome, spondylodysplastic type, 3	.	24
HP:0003301	HP:0003301	Irregular vertebral endplates	0	TCIRG1 CL E G H	10312	11647	ORPHA:1782	Dysosteosclerosis	HP:0040281 - Very frequent	82
HP:0003301	HP:0003301	Irregular vertebral endplates	0	TNFRSF11A CL E G H	8792	11908	ORPHA:1782	Dysosteosclerosis	HP:0040281 - Very frequent	72
HP:0003301	HP:0003301	Irregular vertebral endplates	0	TRAPPC2 CL E G H	6399	23068	ORPHA:93284	Spondyloepiphyseal dysplasia tarda		46
HP:0003301	HP:0003301	Irregular vertebral endplates	0	TRAPPC2 CL E G H	6399	23068	OMIM:313400	Spondyloepiphyseal dysplasia tarda, X-linked		46
HP:0003301	HP:0003301	Irregular vertebral endplates	0	ZBTB20 CL E G H	26137	13503	ORPHA:3042	Intellectual disability-cataracts-calcified pinnae-myopathy syndrome	HP:0040281 - Very frequent	17
HP:0003301	HP:0003301	Irregular vertebral endplates	0	ZBTB20 CL E G H	26137	13503	OMIM:259050	Primrose syndrome	.	17
HP:0003301	HP:0008476	Irregular sclerotic endplates	1	MMP13 CL E G H	4322	7159	OMIM:602111	Spondyloepimetaphyseal dysplasia, Missouri type	.	52
HP:0003301	HP:0008476	Irregular sclerotic endplates	1	POLR3A CL E G H	11128	30074	ORPHA:3455	Wiedemann-Rautenstrauch syndrome	HP:0040282 - Frequent	138
HP:0003301	HP:0004594	Hump-shaped mound of bone in central and posterior portions of vertebral endplate	1	TRAPPC2 CL E G H	6399	23068	ORPHA:93284	Spondyloepiphyseal dysplasia tarda	HP:0040281 - Very frequent	46
HP:0003301	HP:0004594	Hump-shaped mound of bone in central and posterior portions of vertebral endplate	1	TRAPPC2 CL E G H	6399	23068	OMIM:313400	Spondyloepiphyseal dysplasia tarda, X-linked	.	46

Genes (31) :ACP5 B3GALT6 CCN6 CHST3 COL10A1 COL11A1 COL2A1 COL9A1 COL9A2 COL9A3 COMP EIF2AK3 EXOC6B GNPAT GORAB IDH1 KIF22 LOXL3 MMP13 NANS PAPSS2 PDE4D POLR3A RNU4ATAC SLC10A7 SLC29A3 SLC39A13 TCIRG1 TNFRSF11A TRAPPC2 ZBTB20

Diseases (30) :OMIM:607944 OMIM:271640 ORPHA:1159 OMIM:143095 ORPHA:174 OMIM:156500 ORPHA:250984 OMIM:609162 OMIM:604864 OMIM:614135 OMIM:132400 OMIM:226980 OMIM:618395 OMIM:222765 OMIM:231070 ORPHA:99646 OMIM:603546 OMIM:602111 OMIM:610442 OMIM:612847 ORPHA:439822 ORPHA:3455 OMIM:616651 OMIM:618363 ORPHA:1782 OMIM:612350 ORPHA:93284 OMIM:313400 ORPHA:3042 OMIM:259050

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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