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:0003025	HP:0003025	Metaphyseal irregularity	0	ACP5 CL E G H	54	124	OMIM:607944	Spondyloenchondrodysplasia with immune dysregulation	.	16
HP:0003025	HP:0003025	Metaphyseal irregularity	0	ARSB CL E G H	411	714	OMIM:253200	Mucopolysaccharidosis, type VI	.	120
HP:0003025	HP:0003025	Metaphyseal irregularity	0	BGN CL E G H	633	1044	OMIM:300106	Spondyloepimetaphyseal dysplasia, X-linked	.	7
HP:0003025	HP:0003025	Metaphyseal irregularity	0	CASR CL E G H	846	1514	OMIM:239200	Hyperparathyroidism, neonatal severe	.	272
HP:0003025	HP:0003025	Metaphyseal irregularity	0	CFAP410 CL E G H	755	1260	OMIM:602271	Spondylometaphyseal dysplasia, axial
HP:0003025	HP:0003025	Metaphyseal irregularity	0	CLCN5 CL E G H	1184	2023	OMIM:300009	Dent disease 1	.	112
HP:0003025	HP:0003025	Metaphyseal irregularity	0	CLCN5 CL E G H	1184	2023	OMIM:300554	Hypophosphatemic rickets, X-linked recessive	.	112
HP:0003025	HP:0003025	Metaphyseal irregularity	0	COL10A1 CL E G H	1300	2185	ORPHA:174	Metaphyseal chondrodysplasia, Schmid type	HP:0040281 - Very frequent	79
HP:0003025	HP:0003025	Metaphyseal irregularity	0	COL10A1 CL E G H	1300	2185	OMIM:156500	Metaphyseal chondrodysplasia, Schmid type		79
HP:0003025	HP:0003025	Metaphyseal irregularity	0	COL2A1 CL E G H	1280	2200	OMIM:151210	Platyspondylic lethal skeletal dysplasia, Torrance type		284
HP:0003025	HP:0003025	Metaphyseal irregularity	0	COL2A1 CL E G H	1280	2200	OMIM:184250	Spondyloepimetaphyseal dysplasia, Strudwick type	.	284
HP:0003025	HP:0003025	Metaphyseal irregularity	0	COL2A1 CL E G H	1280	2200	ORPHA:93315	Spondylometaphyseal dysplasia, 'corner fracture' type	HP:0040281 - Very frequent	284
HP:0003025	HP:0003025	Metaphyseal irregularity	0	COL2A1 CL E G H	1280	2200	OMIM:184255	Spondylometaphyseal dysplasia, corner Fracture type	.	284
HP:0003025	HP:0003025	Metaphyseal irregularity	0	COMP CL E G H	1311	2227	ORPHA:750	Pseudoachondroplasia	HP:0040282 - Frequent	89
HP:0003025	HP:0003025	Metaphyseal irregularity	0	COMP CL E G H	1311	2227	OMIM:177170	Pseudoachondroplasia		89
HP:0003025	HP:0003025	Metaphyseal irregularity	0	CSPP1 CL E G H	79848	26193	ORPHA:397715	Joubert syndrome with Jeune asphyxiating thoracic dystrophy		57
HP:0003025	HP:0003025	Metaphyseal irregularity	0	CYP27B1 CL E G H	1594	2606	ORPHA:289157	Hypocalcemic vitamin D-dependent rickets		41
HP:0003025	HP:0003025	Metaphyseal irregularity	0	CYP27B1 CL E G H	1594	2606	OMIM:264700	Vitamin D hydroxylation-deficient rickets, type 1A	.	41
HP:0003025	HP:0003025	Metaphyseal irregularity	0	CYP2R1 CL E G H	120227	20580	ORPHA:289157	Hypocalcemic vitamin D-dependent rickets		5
HP:0003025	HP:0003025	Metaphyseal irregularity	0	CYP2R1 CL E G H	120227	20580	OMIM:600081	Vitamin D hydroxylation-deficient rickets, type 1B	.	5
HP:0003025	HP:0003025	Metaphyseal irregularity	0	DDRGK1 CL E G H	65992	16110	OMIM:602557	Spondyloepimetaphyseal dysplasia, Shohat type	.
HP:0003025	HP:0003025	Metaphyseal irregularity	0	DDRGK1 CL E G H	65992	16110	ORPHA:93352	Spondyloepimetaphyseal dysplasia, Shohat type	HP:0040283 - Occasional
HP:0003025	HP:0003025	Metaphyseal irregularity	0	DNAJC21 CL E G H	134218	27030	ORPHA:811	Shwachman-Diamond syndrome	HP:0040283 - Occasional	5
HP:0003025	HP:0003025	Metaphyseal irregularity	0	DNAJC21 CL E G H	134218	27030	OMIM:260400	Shwachman-Diamond syndrome 1		5
HP:0003025	HP:0003025	Metaphyseal irregularity	0	DYM CL E G H	54808	21317	OMIM:607326	Smith-Mccort dysplasia 1	.	65
HP:0003025	HP:0003025	Metaphyseal irregularity	0	EFL1 CL E G H	79631	25789	ORPHA:811	Shwachman-Diamond syndrome	HP:0040283 - Occasional	1
HP:0003025	HP:0003025	Metaphyseal irregularity	0	EFL1 CL E G H	79631	25789	OMIM:617941	Shwachman-Diamond syndrome 2	.	1
HP:0003025	HP:0003025	Metaphyseal irregularity	0	EXOC6B CL E G H	23233	17085	OMIM:618395	Spondyloepimetaphyseal dysplasia with joint laxity, type 3	.	3
HP:0003025	HP:0003025	Metaphyseal irregularity	0	FGFR3 CL E G H	2261	3690	OMIM:187600	Thanatophoric dysplasia, type I	.	145
HP:0003025	HP:0003025	Metaphyseal irregularity	0	FGFR3 CL E G H	2261	3690	OMIM:187601	Thanatophoric dysplasia, type II	.	145
HP:0003025	HP:0003025	Metaphyseal irregularity	0	FN1 CL E G H	2335	3778	ORPHA:93315	Spondylometaphyseal dysplasia, 'corner fracture' type	HP:0040281 - Very frequent	9
HP:0003025	HP:0003025	Metaphyseal irregularity	0	FN1 CL E G H	2335	3778	OMIM:184255	Spondylometaphyseal dysplasia, corner Fracture type	.	9
HP:0003025	HP:0003025	Metaphyseal irregularity	0	GPX4 CL E G H	2879	4556	OMIM:250220	Spondylometaphyseal dysplasia, Sedaghatian type	.	3
HP:0003025	HP:0003025	Metaphyseal irregularity	0	IARS2 CL E G H	55699	29685	OMIM:616007	Cataracts, growth hormone deficiency, sensory neuropathy, sensorineural hearing loss, and skeletal dysplasia	.	25
HP:0003025	HP:0003025	Metaphyseal irregularity	0	IDH1 CL E G H	3417	5382	ORPHA:99646	Metaphyseal chondromatosis with D-2-hydroxyglutaric aciduria		15
HP:0003025	HP:0003025	Metaphyseal irregularity	0	KIAA0586 CL E G H	9786	19960	ORPHA:397715	Joubert syndrome with Jeune asphyxiating thoracic dystrophy		24
HP:0003025	HP:0003025	Metaphyseal irregularity	0	KIF22 CL E G H	3835	6391	OMIM:603546	Spondyloepimetaphyseal dysplasia with joint laxity, type 2	.	14
HP:0003025	HP:0003025	Metaphyseal irregularity	0	KIF22 CL E G H	3835	6391	ORPHA:93360	Spondyloepimetaphyseal dysplasia with multiple dislocations	HP:0040282 - Frequent	14
HP:0003025	HP:0003025	Metaphyseal irregularity	0	LBR CL E G H	3930	6518	OMIM:618019	PELGER-HUET ANOMALY WITH MILD SKELETAL ANOMALIES; PHASK		70
HP:0003025	HP:0003025	Metaphyseal irregularity	0	LPIN2 CL E G H	9663	14450	ORPHA:77297	Majeed syndrome	HP:0040281 - Very frequent	186
HP:0003025	HP:0003025	Metaphyseal irregularity	0	MATN3 CL E G H	4148	6909	OMIM:607078	Epiphyseal dysplasia, multiple, 5	.	32
HP:0003025	HP:0003025	Metaphyseal irregularity	0	MMP13 CL E G H	4322	7159	ORPHA:93356	Spondyloepimetaphyseal dysplasia, Missouri type	HP:0040282 - Frequent	52
HP:0003025	HP:0003025	Metaphyseal irregularity	0	MMP9 CL E G H	4318	7176	OMIM:613073	METAPHYSEAL ANADYSPLASIA 2; MANDP2		31
HP:0003025	HP:0003025	Metaphyseal irregularity	0	NANS CL E G H	54187	19237	OMIM:610442	Spondyloepimetaphyseal dysplasia, Genevieve type	.	8
HP:0003025	HP:0003025	Metaphyseal irregularity	0	NKX3-2 CL E G H	579	951	OMIM:613330	Spondylo-Megaepiphyseal-Metaphyseal dysplasia	.	10
HP:0003025	HP:0003025	Metaphyseal irregularity	0	PCYT1A CL E G H	5130	8754	OMIM:608940	Spondylometaphyseal dysplasia with cone-rod dystrophy		11
HP:0003025	HP:0003025	Metaphyseal irregularity	0	PCYT1A CL E G H	5130	8754	ORPHA:85167	Spondylometaphyseal dysplasia-cone-rod dystrophy syndrome	HP:0040281 - Very frequent	11
HP:0003025	HP:0003025	Metaphyseal irregularity	0	PEX5 CL E G H	5830	9719	OMIM:616716	RHIZOMELIC CHONDRODYSPLASIA PUNCTATA, TYPE 5; RCDP5		99
HP:0003025	HP:0003025	Metaphyseal irregularity	0	PHEX CL E G H	5251	8918	OMIM:307800	Hypophosphatemic rickets, X-linked dominant	.	217
HP:0003025	HP:0003025	Metaphyseal irregularity	0	PRKG2 CL E G H	5593	9416	OMIM:619636	ACROMESOMELIC DYSPLASIA 4; AMD4
HP:0003025	HP:0003025	Metaphyseal irregularity	0	PTH1R CL E G H	5745	9608	ORPHA:79106	Eiken syndrome	HP:0040282 - Frequent	58
HP:0003025	HP:0003025	Metaphyseal irregularity	0	QRICH1 CL E G H	54870	24713	OMIM:617982	VERVERI-BRADY SYNDROME; VERBRAS
HP:0003025	HP:0003025	Metaphyseal irregularity	0	RAB33B CL E G H	83452	16075	OMIM:615222	Smith-Mccort dysplasia 2	.	53
HP:0003025	HP:0003025	Metaphyseal irregularity	0	RMRP CL E G H	6023	10031	OMIM:250460	Metaphyseal dysplasia without hypotrichosis	.	37
HP:0003025	HP:0003025	Metaphyseal irregularity	0	RPL13 CL E G H	6137	10303	OMIM:618728	SPONDYLOEPIMETAPHYSEAL DYSPLASIA, ISIDOR-TOUTAIN TYPE; SEMDIST
HP:0003025	HP:0003025	Metaphyseal irregularity	0	RSPRY1 CL E G H	89970	29420	ORPHA:457395	Progressive spondyloepimetaphyseal dysplasia-short stature-short fourth metatarsals-intellectual disability syndrome		2
HP:0003025	HP:0003025	Metaphyseal irregularity	0	SBDS CL E G H	51119	19440	ORPHA:811	Shwachman-Diamond syndrome	HP:0040283 - Occasional	26
HP:0003025	HP:0003025	Metaphyseal irregularity	0	SBDS CL E G H	51119	19440	OMIM:260400	Shwachman-Diamond syndrome 1		26
HP:0003025	HP:0003025	Metaphyseal irregularity	0	SIK3 CL E G H	23387	29165	OMIM:618162	Spondyloepimetaphyseal dysplasia, Krakow type	.
HP:0003025	HP:0003025	Metaphyseal irregularity	0	SLC17A5 CL E G H	26503	10933	OMIM:269920	Infantile sialic acid storage disease	.	78
HP:0003025	HP:0003025	Metaphyseal irregularity	0	SLC34A3 CL E G H	142680	20305	OMIM:241530	Hypophosphatemic rickets with hypercalciuria, hereditary	.	52
HP:0003025	HP:0003025	Metaphyseal irregularity	0	SLC35D1 CL E G H	23169	20800	OMIM:269250	Schneckenbecken dysplasia	.	9
HP:0003025	HP:0003025	Metaphyseal irregularity	0	SRP54 CL E G H	6729	11301	ORPHA:811	Shwachman-Diamond syndrome	HP:0040283 - Occasional
HP:0003025	HP:0003025	Metaphyseal irregularity	0	SRP54 CL E G H	6729	11301	OMIM:260400	Shwachman-Diamond syndrome 1
HP:0003025	HP:0003025	Metaphyseal irregularity	0	TONSL CL E G H	4796	7801	ORPHA:93357	SPONASTRIME dysplasia	HP:0040282 - Frequent
HP:0003025	HP:0003025	Metaphyseal irregularity	0	TONSL CL E G H	4796	7801	OMIM:271510	Spondyloepimetaphyseal dysplasia, Sponastrime type	.
HP:0003025	HP:0003025	Metaphyseal irregularity	0	TRPV4 CL E G H	59341	18083	OMIM:113500	Brachyolmia type 3		214
HP:0003025	HP:0003025	Metaphyseal irregularity	0	TRPV4 CL E G H	59341	18083	OMIM:156530	Metatropic dysplasia		214
HP:0003025	HP:0003025	Metaphyseal irregularity	0	TRPV4 CL E G H	59341	18083	OMIM:184252	Spondylometaphyseal dysplasia, Kozlowski type		214
HP:0003025	HP:0003025	Metaphyseal irregularity	0	VDR CL E G H	7421	12679	OMIM:277440	Vitamin d-dependent rickets, type 2A	.	104
HP:0003025	HP:0030291	Lower-limb metaphyseal irregularity	1	CFAP410 CL E G H	755	1260	OMIM:602271	Spondylometaphyseal dysplasia, axial
HP:0003025	HP:0030291	Lower-limb metaphyseal irregularity	1	COL10A1 CL E G H	1300	2185	ORPHA:174	Metaphyseal chondrodysplasia, Schmid type		79
HP:0003025	HP:0003850	Upper-limb metaphyseal irregularity	1	COL10A1 CL E G H	1300	2185	ORPHA:174	Metaphyseal chondrodysplasia, Schmid type		79
HP:0003025	HP:0003850	Upper-limb metaphyseal irregularity	1	COMP CL E G H	1311	2227	OMIM:177170	Pseudoachondroplasia		89
HP:0003025	HP:0030291	Lower-limb metaphyseal irregularity	1	CSPP1 CL E G H	79848	26193	ORPHA:397715	Joubert syndrome with Jeune asphyxiating thoracic dystrophy		57
HP:0003025	HP:0005042	Irregular, rachitic-like metaphyses	1	CYP27B1 CL E G H	1594	2606	ORPHA:289157	Hypocalcemic vitamin D-dependent rickets	HP:0040281 - Very frequent	41
HP:0003025	HP:0005042	Irregular, rachitic-like metaphyses	1	CYP2R1 CL E G H	120227	20580	ORPHA:289157	Hypocalcemic vitamin D-dependent rickets	HP:0040281 - Very frequent	5
HP:0003025	HP:0030291	Lower-limb metaphyseal irregularity	1	DNAJC21 CL E G H	134218	27030	OMIM:260400	Shwachman-Diamond syndrome 1		5
HP:0003025	HP:0030291	Lower-limb metaphyseal irregularity	1	KIAA0586 CL E G H	9786	19960	ORPHA:397715	Joubert syndrome with Jeune asphyxiating thoracic dystrophy		24
HP:0003025	HP:0030291	Lower-limb metaphyseal irregularity	1	RPL13 CL E G H	6137	10303	OMIM:618728	SPONDYLOEPIMETAPHYSEAL DYSPLASIA, ISIDOR-TOUTAIN TYPE; SEMDIST
HP:0003025	HP:0003850	Upper-limb metaphyseal irregularity	1	RPL13 CL E G H	6137	10303	OMIM:618728	SPONDYLOEPIMETAPHYSEAL DYSPLASIA, ISIDOR-TOUTAIN TYPE; SEMDIST
HP:0003025	HP:0030291	Lower-limb metaphyseal irregularity	1	RSPRY1 CL E G H	89970	29420	ORPHA:457395	Progressive spondyloepimetaphyseal dysplasia-short stature-short fourth metatarsals-intellectual disability syndrome		2
HP:0003025	HP:0030291	Lower-limb metaphyseal irregularity	1	SBDS CL E G H	51119	19440	OMIM:260400	Shwachman-Diamond syndrome 1		26
HP:0003025	HP:0030291	Lower-limb metaphyseal irregularity	1	SRP54 CL E G H	6729	11301	OMIM:260400	Shwachman-Diamond syndrome 1
HP:0003025	HP:0030291	Lower-limb metaphyseal irregularity	1	TRPV4 CL E G H	59341	18083	OMIM:113500	Brachyolmia type 3		214
HP:0003025	HP:0005042	Irregular, rachitic-like metaphyses	1	TRPV4 CL E G H	59341	18083	OMIM:184252	Spondylometaphyseal dysplasia, Kozlowski type	.	214
HP:0003025	HP:0003913	Humeral metaphyseal irregularity	2	CL E G H
HP:0003025	HP:0003411	Proximal femoral metaphyseal irregularity	2	CFAP410 CL E G H	755	1260	OMIM:602271	Spondylometaphyseal dysplasia, axial	.
HP:0003025	HP:0004042	Ulnar metaphyseal irregularity	2	COL10A1 CL E G H	1300	2185	ORPHA:174	Metaphyseal chondrodysplasia, Schmid type	HP:0040283 - Occasional	79
HP:0003025	HP:0045079	Distal femoral metaphyseal irregularity	2	COL10A1 CL E G H	1300	2185	ORPHA:174	Metaphyseal chondrodysplasia, Schmid type	HP:0040282 - Frequent	79
HP:0003025	HP:0004019	Radial metaphyseal irregularity	2	COL10A1 CL E G H	1300	2185	ORPHA:174	Metaphyseal chondrodysplasia, Schmid type	HP:0040283 - Occasional	79
HP:0003025	HP:0003411	Proximal femoral metaphyseal irregularity	2	COL10A1 CL E G H	1300	2185	ORPHA:174	Metaphyseal chondrodysplasia, Schmid type	HP:0040282 - Frequent	79
HP:0003025	HP:0004019	Radial metaphyseal irregularity	2	COMP CL E G H	1311	2227	OMIM:177170	Pseudoachondroplasia		89
HP:0003025	HP:0004042	Ulnar metaphyseal irregularity	2	COMP CL E G H	1311	2227	OMIM:177170	Pseudoachondroplasia		89
HP:0003025	HP:0003411	Proximal femoral metaphyseal irregularity	2	CSPP1 CL E G H	79848	26193	ORPHA:397715	Joubert syndrome with Jeune asphyxiating thoracic dystrophy	HP:0040283 - Occasional	57
HP:0003025	HP:0003411	Proximal femoral metaphyseal irregularity	2	DNAJC21 CL E G H	134218	27030	OMIM:260400	Shwachman-Diamond syndrome 1		5
HP:0003025	HP:0003411	Proximal femoral metaphyseal irregularity	2	KIAA0586 CL E G H	9786	19960	ORPHA:397715	Joubert syndrome with Jeune asphyxiating thoracic dystrophy	HP:0040283 - Occasional	24
HP:0003025	HP:0030293	Fibular metaphyseal irregularity	2	RSPRY1 CL E G H	89970	29420	ORPHA:457395	Progressive spondyloepimetaphyseal dysplasia-short stature-short fourth metatarsals-intellectual disability syndrome	HP:0040282 - Frequent	2
HP:0003025	HP:0030292	Tibial metaphyseal irregularity	2	RSPRY1 CL E G H	89970	29420	ORPHA:457395	Progressive spondyloepimetaphyseal dysplasia-short stature-short fourth metatarsals-intellectual disability syndrome	HP:0040282 - Frequent	2
HP:0003025	HP:0003411	Proximal femoral metaphyseal irregularity	2	SBDS CL E G H	51119	19440	OMIM:260400	Shwachman-Diamond syndrome 1		26
HP:0003025	HP:0003411	Proximal femoral metaphyseal irregularity	2	SRP54 CL E G H	6729	11301	OMIM:260400	Shwachman-Diamond syndrome 1
HP:0003025	HP:0003411	Proximal femoral metaphyseal irregularity	2	TRPV4 CL E G H	59341	18083	OMIM:113500	Brachyolmia type 3	.	214
HP:0003025	HP:0003951	Distal humeral metaphyseal irregularity	3	CL E G H
HP:0003025	HP:0005043	Proximal humeral metaphyseal irregularity	3	CL E G H