Human Phenotype Ontology

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:0005106	HP:0005106	Abnormality of the vertebral endplates	0	ACP5 CL E G H	54	124	OMIM:607944	Spondyloenchondrodysplasia with immune dysregulation		16
HP:0005106	HP:0005106	Abnormality of the 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:0005106	HP:0005106	Abnormality of the vertebral endplates	0	CCN6 CL E G H	8838	12771	OMIM:208230	Arthropathy, progressive pseudorheumatoid, of childhood
HP:0005106	HP:0005106	Abnormality of the vertebral endplates	0	CCN6 CL E G H	8838	12771	ORPHA:1159	Progressive pseudorheumatoid arthropathy of childhood
HP:0005106	HP:0005106	Abnormality of the vertebral endplates	0	CHST3 CL E G H	9469	1971	OMIM:143095	Spondyloepiphyseal dysplasia with congenital joint dislocations		165
HP:0005106	HP:0005106	Abnormality of the vertebral endplates	0	CLCN7 CL E G H	1186	2025	OMIM:166600	Osteopetrosis, autosomal dominant 2	.	102
HP:0005106	HP:0005106	Abnormality of the vertebral endplates	0	CLCN7 CL E G H	1186	2025	OMIM:611490	Osteopetrosis, autosomal recessive 4		102
HP:0005106	HP:0005106	Abnormality of the vertebral endplates	0	COL10A1 CL E G H	1300	2185	ORPHA:174	Metaphyseal chondrodysplasia, Schmid type		79
HP:0005106	HP:0005106	Abnormality of the vertebral endplates	0	COL10A1 CL E G H	1300	2185	OMIM:156500	Metaphyseal chondrodysplasia, Schmid type		79
HP:0005106	HP:0005106	Abnormality of the vertebral endplates	0	COL11A1 CL E G H	1301	2186	ORPHA:250984	Autosomal recessive Stickler syndrome		215
HP:0005106	HP:0005106	Abnormality of the vertebral endplates	0	COL2A1 CL E G H	1280	2200	OMIM:609162	Czech dysplasia, Metatarsal type		284
HP:0005106	HP:0005106	Abnormality of the vertebral endplates	0	COL2A1 CL E G H	1280	2200	OMIM:604864	Osteoarthritis with mild chondrodysplasia		284
HP:0005106	HP:0005106	Abnormality of the vertebral endplates	0	COL2A1 CL E G H	1280	2200	OMIM:184255	Spondylometaphyseal dysplasia, corner Fracture type		284
HP:0005106	HP:0005106	Abnormality of the vertebral endplates	0	COL2A1 CL E G H	1280	2200	ORPHA:1856	Spondyloperipheral dysplasia-short ulna syndrome	HP:0040282 - Frequent	284
HP:0005106	HP:0005106	Abnormality of the vertebral endplates	0	COL9A1 CL E G H	1297	2217	ORPHA:250984	Autosomal recessive Stickler syndrome		110
HP:0005106	HP:0005106	Abnormality of the vertebral endplates	0	COL9A1 CL E G H	1297	2217	OMIM:614135	Epiphyseal dysplasia, multiple, 6		110
HP:0005106	HP:0005106	Abnormality of the vertebral endplates	0	COL9A2 CL E G H	1298	2218	ORPHA:250984	Autosomal recessive Stickler syndrome		110
HP:0005106	HP:0005106	Abnormality of the vertebral endplates	0	COL9A3 CL E G H	1299	2219	ORPHA:250984	Autosomal recessive Stickler syndrome		137
HP:0005106	HP:0005106	Abnormality of the vertebral endplates	0	COMP CL E G H	1311	2227	OMIM:132400	Epiphyseal dysplasia, multiple, 1		89
HP:0005106	HP:0005106	Abnormality of the vertebral endplates	0	DMP1 CL E G H	1758	2932	ORPHA:289176	Autosomal recessive hypophosphatemic rickets		48
HP:0005106	HP:0005106	Abnormality of the vertebral endplates	0	DYM CL E G H	54808	21317	ORPHA:239	Dyggve-Melchior-Clausen disease	HP:0040282 - Frequent	65
HP:0005106	HP:0005106	Abnormality of the vertebral endplates	0	EIF2AK3 CL E G H	9451	3255	OMIM:226980	Epiphyseal dysplasia, multiple, with early-onset diabetes mellitus		65
HP:0005106	HP:0005106	Abnormality of the vertebral endplates	0	ENPP1 CL E G H	5167	3356	ORPHA:289176	Autosomal recessive hypophosphatemic rickets		151
HP:0005106	HP:0005106	Abnormality of the vertebral endplates	0	EXOC6B CL E G H	23233	17085	OMIM:618395	Spondyloepimetaphyseal dysplasia with joint laxity, type 3		3
HP:0005106	HP:0005106	Abnormality of the vertebral endplates	0	FN1 CL E G H	2335	3778	OMIM:184255	Spondylometaphyseal dysplasia, corner Fracture type		9
HP:0005106	HP:0005106	Abnormality of the vertebral endplates	0	GNPAT CL E G H	8443	4416	OMIM:222765	Rhizomelic chondrodysplasia punctata, type 2		58
HP:0005106	HP:0005106	Abnormality of the vertebral endplates	0	GORAB CL E G H	92344	25676	OMIM:231070	Geroderma osteodysplasticum		52
HP:0005106	HP:0005106	Abnormality of the vertebral endplates	0	IDH1 CL E G H	3417	5382	ORPHA:99646	Metaphyseal chondromatosis with D-2-hydroxyglutaric aciduria		15
HP:0005106	HP:0005106	Abnormality of the vertebral endplates	0	KIF22 CL E G H	3835	6391	OMIM:603546	Spondyloepimetaphyseal dysplasia with joint laxity, type 2		14
HP:0005106	HP:0005106	Abnormality of the vertebral endplates	0	LOXL3 CL E G H	84695	13869	ORPHA:250984	Autosomal recessive Stickler syndrome		4
HP:0005106	HP:0005106	Abnormality of the vertebral endplates	0	LRRK1 CL E G H	79705	18608	OMIM:615198	Osteosclerotic metaphyseal dysplasia		1
HP:0005106	HP:0005106	Abnormality of the vertebral endplates	0	MMP13 CL E G H	4322	7159	OMIM:602111	Spondyloepimetaphyseal dysplasia, Missouri type		52
HP:0005106	HP:0005106	Abnormality of the vertebral endplates	0	NANS CL E G H	54187	19237	OMIM:610442	Spondyloepimetaphyseal dysplasia, Genevieve type		8
HP:0005106	HP:0005106	Abnormality of the vertebral endplates	0	PAPSS2 CL E G H	9060	8604	OMIM:612847	Brachyolmia 4 with mild epiphyseal and metaphyseal changes		20
HP:0005106	HP:0005106	Abnormality of the vertebral endplates	0	PDE4D CL E G H	5144	8783	ORPHA:439822	PDE4D haploinsufficiency syndrome		113
HP:0005106	HP:0005106	Abnormality of the vertebral endplates	0	POLR3A CL E G H	11128	30074	ORPHA:3455	Wiedemann-Rautenstrauch syndrome		138
HP:0005106	HP:0005106	Abnormality of the vertebral endplates	0	RNU4ATAC CL E G H	100151683	34016	OMIM:616651	Roifman syndrome		15
HP:0005106	HP:0005106	Abnormality of the vertebral endplates	0	SLC10A7 CL E G H	84068	23088	OMIM:618363	Short stature, amelogenesis imperfecta, and skeletal dysplasia with scoliosis
HP:0005106	HP:0005106	Abnormality of the vertebral endplates	0	SLC29A3 CL E G H	55315	23096	ORPHA:1782	Dysosteosclerosis		68
HP:0005106	HP:0005106	Abnormality of the vertebral endplates	0	SLC39A13 CL E G H	91252	20859	OMIM:612350	Ehlers-Danlos syndrome, spondylodysplastic type, 3		24
HP:0005106	HP:0005106	Abnormality of the vertebral endplates	0	SOST CL E G H	50964	13771	OMIM:269500	Sclerosteosis 1		26
HP:0005106	HP:0005106	Abnormality of the vertebral endplates	0	TCIRG1 CL E G H	10312	11647	ORPHA:1782	Dysosteosclerosis		82
HP:0005106	HP:0005106	Abnormality of the vertebral endplates	0	TNFRSF11A CL E G H	8792	11908	ORPHA:1782	Dysosteosclerosis		72
HP:0005106	HP:0005106	Abnormality of the vertebral endplates	0	TONSL CL E G H	4796	7801	ORPHA:93357	SPONASTRIME dysplasia
HP:0005106	HP:0005106	Abnormality of the vertebral endplates	0	TRAPPC2 CL E G H	6399	23068	ORPHA:93284	Spondyloepiphyseal dysplasia tarda		46
HP:0005106	HP:0005106	Abnormality of the vertebral endplates	0	TRAPPC2 CL E G H	6399	23068	OMIM:313400	Spondyloepiphyseal dysplasia tarda, X-linked		46
HP:0005106	HP:0005106	Abnormality of the vertebral endplates	0	ZBTB20 CL E G H	26137	13503	ORPHA:3042	Intellectual disability-cataracts-calcified pinnae-myopathy syndrome		17
HP:0005106	HP:0005106	Abnormality of the vertebral endplates	0	ZBTB20 CL E G H	26137	13503	OMIM:259050	Primrose syndrome		17
HP:0005106	HP:0003301	Irregular vertebral endplates	1	ACP5 CL E G H	54	124	OMIM:607944	Spondyloenchondrodysplasia with immune dysregulation	.	16
HP:0005106	HP:0003301	Irregular vertebral endplates	1	B3GALT6 CL E G H	126792	17978	OMIM:271640	Spondyloepimetaphyseal dysplasia with joint laxity, type 1, with or without fractures	.	38
HP:0005106	HP:0004576	Sclerotic vertebral endplates	1	CCN6 CL E G H	8838	12771	OMIM:208230	Arthropathy, progressive pseudorheumatoid, of childhood	.
HP:0005106	HP:0004603	Hyperconvex vertebral body endplates	1	CCN6 CL E G H	8838	12771	ORPHA:1159	Progressive pseudorheumatoid arthropathy of childhood	HP:0040282 - Frequent
HP:0005106	HP:0003301	Irregular vertebral endplates	1	CCN6 CL E G H	8838	12771	ORPHA:1159	Progressive pseudorheumatoid arthropathy of childhood	HP:0040281 - Very frequent
HP:0005106	HP:0003301	Irregular vertebral endplates	1	CHST3 CL E G H	9469	1971	OMIM:143095	Spondyloepiphyseal dysplasia with congenital joint dislocations	.	165
HP:0005106	HP:0004576	Sclerotic vertebral endplates	1	CLCN7 CL E G H	1186	2025	OMIM:611490	Osteopetrosis, autosomal recessive 4	.	102
HP:0005106	HP:0003301	Irregular vertebral endplates	1	COL10A1 CL E G H	1300	2185	ORPHA:174	Metaphyseal chondrodysplasia, Schmid type	HP:0040283 - Occasional	79
HP:0005106	HP:0003301	Irregular vertebral endplates	1	COL10A1 CL E G H	1300	2185	OMIM:156500	Metaphyseal chondrodysplasia, Schmid type	.	79
HP:0005106	HP:0003301	Irregular vertebral endplates	1	COL11A1 CL E G H	1301	2186	ORPHA:250984	Autosomal recessive Stickler syndrome	HP:0040282 - Frequent	215
HP:0005106	HP:0003301	Irregular vertebral endplates	1	COL2A1 CL E G H	1280	2200	OMIM:609162	Czech dysplasia, Metatarsal type	.	284
HP:0005106	HP:0003301	Irregular vertebral endplates	1	COL2A1 CL E G H	1280	2200	OMIM:604864	Osteoarthritis with mild chondrodysplasia	.	284
HP:0005106	HP:0004603	Hyperconvex vertebral body endplates	1	COL2A1 CL E G H	1280	2200	OMIM:184255	Spondylometaphyseal dysplasia, corner Fracture type	.	284
HP:0005106	HP:0003301	Irregular vertebral endplates	1	COL9A1 CL E G H	1297	2217	ORPHA:250984	Autosomal recessive Stickler syndrome	HP:0040282 - Frequent	110
HP:0005106	HP:0003301	Irregular vertebral endplates	1	COL9A1 CL E G H	1297	2217	OMIM:614135	Epiphyseal dysplasia, multiple, 6		110
HP:0005106	HP:0003301	Irregular vertebral endplates	1	COL9A2 CL E G H	1298	2218	ORPHA:250984	Autosomal recessive Stickler syndrome	HP:0040282 - Frequent	110
HP:0005106	HP:0003301	Irregular vertebral endplates	1	COL9A3 CL E G H	1299	2219	ORPHA:250984	Autosomal recessive Stickler syndrome	HP:0040282 - Frequent	137
HP:0005106	HP:0003301	Irregular vertebral endplates	1	COMP CL E G H	1311	2227	OMIM:132400	Epiphyseal dysplasia, multiple, 1	.	89
HP:0005106	HP:0004576	Sclerotic vertebral endplates	1	DMP1 CL E G H	1758	2932	ORPHA:289176	Autosomal recessive hypophosphatemic rickets	HP:0040281 - Very frequent	48
HP:0005106	HP:0003301	Irregular vertebral endplates	1	EIF2AK3 CL E G H	9451	3255	OMIM:226980	Epiphyseal dysplasia, multiple, with early-onset diabetes mellitus	.	65
HP:0005106	HP:0004576	Sclerotic vertebral endplates	1	ENPP1 CL E G H	5167	3356	ORPHA:289176	Autosomal recessive hypophosphatemic rickets	HP:0040281 - Very frequent	151
HP:0005106	HP:0003301	Irregular vertebral endplates	1	EXOC6B CL E G H	23233	17085	OMIM:618395	Spondyloepimetaphyseal dysplasia with joint laxity, type 3	.	3
HP:0005106	HP:0004603	Hyperconvex vertebral body endplates	1	FN1 CL E G H	2335	3778	OMIM:184255	Spondylometaphyseal dysplasia, corner Fracture type	.	9
HP:0005106	HP:0003301	Irregular vertebral endplates	1	GNPAT CL E G H	8443	4416	OMIM:222765	Rhizomelic chondrodysplasia punctata, type 2	.	58
HP:0005106	HP:0003301	Irregular vertebral endplates	1	GORAB CL E G H	92344	25676	OMIM:231070	Geroderma osteodysplasticum	.	52
HP:0005106	HP:0003301	Irregular vertebral endplates	1	IDH1 CL E G H	3417	5382	ORPHA:99646	Metaphyseal chondromatosis with D-2-hydroxyglutaric aciduria		15
HP:0005106	HP:0003301	Irregular vertebral endplates	1	KIF22 CL E G H	3835	6391	OMIM:603546	Spondyloepimetaphyseal dysplasia with joint laxity, type 2	.	14
HP:0005106	HP:0003301	Irregular vertebral endplates	1	LOXL3 CL E G H	84695	13869	ORPHA:250984	Autosomal recessive Stickler syndrome	HP:0040282 - Frequent	4
HP:0005106	HP:0004576	Sclerotic vertebral endplates	1	LRRK1 CL E G H	79705	18608	OMIM:615198	Osteosclerotic metaphyseal dysplasia		1
HP:0005106	HP:0003301	Irregular vertebral endplates	1	MMP13 CL E G H	4322	7159	OMIM:602111	Spondyloepimetaphyseal dysplasia, Missouri type		52
HP:0005106	HP:0003301	Irregular vertebral endplates	1	NANS CL E G H	54187	19237	OMIM:610442	Spondyloepimetaphyseal dysplasia, Genevieve type	.	8
HP:0005106	HP:0003301	Irregular vertebral endplates	1	PAPSS2 CL E G H	9060	8604	OMIM:612847	Brachyolmia 4 with mild epiphyseal and metaphyseal changes	.	20
HP:0005106	HP:0003301	Irregular vertebral endplates	1	PDE4D CL E G H	5144	8783	ORPHA:439822	PDE4D haploinsufficiency syndrome	HP:0040283 - Occasional	113
HP:0005106	HP:0003301	Irregular vertebral endplates	1	POLR3A CL E G H	11128	30074	ORPHA:3455	Wiedemann-Rautenstrauch syndrome		138
HP:0005106	HP:0003301	Irregular vertebral endplates	1	RNU4ATAC CL E G H	100151683	34016	OMIM:616651	Roifman syndrome	.	15
HP:0005106	HP:0003301	Irregular vertebral endplates	1	SLC10A7 CL E G H	84068	23088	OMIM:618363	Short stature, amelogenesis imperfecta, and skeletal dysplasia with scoliosis	.
HP:0005106	HP:0003301	Irregular vertebral endplates	1	SLC29A3 CL E G H	55315	23096	ORPHA:1782	Dysosteosclerosis	HP:0040281 - Very frequent	68
HP:0005106	HP:0003301	Irregular vertebral endplates	1	SLC39A13 CL E G H	91252	20859	OMIM:612350	Ehlers-Danlos syndrome, spondylodysplastic type, 3	.	24
HP:0005106	HP:0004576	Sclerotic vertebral endplates	1	SOST CL E G H	50964	13771	OMIM:269500	Sclerosteosis 1	.	26
HP:0005106	HP:0003301	Irregular vertebral endplates	1	TCIRG1 CL E G H	10312	11647	ORPHA:1782	Dysosteosclerosis	HP:0040281 - Very frequent	82
HP:0005106	HP:0003301	Irregular vertebral endplates	1	TNFRSF11A CL E G H	8792	11908	ORPHA:1782	Dysosteosclerosis	HP:0040281 - Very frequent	72
HP:0005106	HP:0004603	Hyperconvex vertebral body endplates	1	TONSL CL E G H	4796	7801	ORPHA:93357	SPONASTRIME dysplasia	HP:0040283 - Occasional
HP:0005106	HP:0003301	Irregular vertebral endplates	1	TRAPPC2 CL E G H	6399	23068	ORPHA:93284	Spondyloepiphyseal dysplasia tarda		46
HP:0005106	HP:0003301	Irregular vertebral endplates	1	TRAPPC2 CL E G H	6399	23068	OMIM:313400	Spondyloepiphyseal dysplasia tarda, X-linked		46
HP:0005106	HP:0003301	Irregular vertebral endplates	1	ZBTB20 CL E G H	26137	13503	ORPHA:3042	Intellectual disability-cataracts-calcified pinnae-myopathy syndrome	HP:0040281 - Very frequent	17
HP:0005106	HP:0003301	Irregular vertebral endplates	1	ZBTB20 CL E G H	26137	13503	OMIM:259050	Primrose syndrome	.	17
HP:0005106	HP:0008476	Irregular sclerotic endplates	2	MMP13 CL E G H	4322	7159	OMIM:602111	Spondyloepimetaphyseal dysplasia, Missouri type	.	52
HP:0005106	HP:0008476	Irregular sclerotic endplates	2	POLR3A CL E G H	11128	30074	ORPHA:3455	Wiedemann-Rautenstrauch syndrome	HP:0040282 - Frequent	138
HP:0005106	HP:0004594	Hump-shaped mound of bone in central and posterior portions of vertebral endplate	2	TRAPPC2 CL E G H	6399	23068	ORPHA:93284	Spondyloepiphyseal dysplasia tarda	HP:0040281 - Very frequent	46
HP:0005106	HP:0004594	Hump-shaped mound of bone in central and posterior portions of vertebral endplate	2	TRAPPC2 CL E G H	6399	23068	OMIM:313400	Spondyloepiphyseal dysplasia tarda, X-linked	.	46