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:0002703	HP:0002703	Abnormality of skull ossification	0	ALG9 CL E G H	79796	15672	OMIM:263210	Gillessen-Kaesbach-Nishimura syndrome		93
HP:0002703	HP:0002703	Abnormality of skull ossification	0	ALPL CL E G H	249	438	OMIM:241500	Hypophosphatasia, infantile		126
HP:0002703	HP:0002703	Abnormality of skull ossification	0	ALX4 CL E G H	60529	450	ORPHA:52022	Potocki-Shaffer syndrome		132
HP:0002703	HP:0002703	Abnormality of skull ossification	0	ANTXR1 CL E G H	84168	21014	ORPHA:2067	GAPO syndrome		8
HP:0002703	HP:0002703	Abnormality of skull ossification	0	BMPER CL E G H	168667	24154	OMIM:608022	DIAPHANOSPONDYLODYSOSTOSIS		78
HP:0002703	HP:0002703	Abnormality of skull ossification	0	COL1A1 CL E G H	1277	2197	OMIM:166210	Osteogenesis imperfecta, type IIA		373
HP:0002703	HP:0002703	Abnormality of skull ossification	0	COL1A1 CL E G H	1277	2197	OMIM:259420	Osteogenesis imperfecta, type III		373
HP:0002703	HP:0002703	Abnormality of skull ossification	0	COL1A2 CL E G H	1278	2198	OMIM:166210	Osteogenesis imperfecta, type IIA		243
HP:0002703	HP:0002703	Abnormality of skull ossification	0	COL1A2 CL E G H	1278	2198	OMIM:259420	Osteogenesis imperfecta, type III		243
HP:0002703	HP:0002703	Abnormality of skull ossification	0	COL2A1 CL E G H	1280	2200	OMIM:151210	Platyspondylic lethal skeletal dysplasia, Torrance type		284
HP:0002703	HP:0002703	Abnormality of skull ossification	0	CREB3L1 CL E G H	90993	18856	OMIM:616229	Osteogenesis imperfecta, type XVI		4
HP:0002703	HP:0002703	Abnormality of skull ossification	0	CRTAP CL E G H	10491	2379	OMIM:610682	Osteogenesis imperfecta, type VII		124
HP:0002703	HP:0002703	Abnormality of skull ossification	0	CSF1R CL E G H	1436	2433	OMIM:618476	Brain abnormalities, neurodegeneration, and dysosteosclerosis		149
HP:0002703	HP:0002703	Abnormality of skull ossification	0	EXT2 CL E G H	2132	3513	ORPHA:52022	Potocki-Shaffer syndrome		102
HP:0002703	HP:0002703	Abnormality of skull ossification	0	FAM111A CL E G H	63901	24725	ORPHA:93325	Autosomal dominant Kenny-Caffey syndrome		8
HP:0002703	HP:0002703	Abnormality of skull ossification	0	FAM111A CL E G H	63901	24725	OMIM:602361	Gracile bone dysplasia		8
HP:0002703	HP:0002703	Abnormality of skull ossification	0	FGFR2 CL E G H	2263	3689	ORPHA:313855	FGFR2-related bent bone dysplasia		175
HP:0002703	HP:0002703	Abnormality of skull ossification	0	FIG4 CL E G H	9896	16873	ORPHA:3472	Yunis-Varon syndrome		111
HP:0002703	HP:0002703	Abnormality of skull ossification	0	FIG4 CL E G H	9896	16873	OMIM:216340	Yunis-Varon syndrome		111
HP:0002703	HP:0002703	Abnormality of skull ossification	0	HDAC6 CL E G H	10013	14064	OMIM:300863	Chondrodysplasia with platyspondyly, distinctive brachydactyly, hydrocephaly, and microphthalmia		2
HP:0002703	HP:0002703	Abnormality of skull ossification	0	HGSNAT CL E G H	138050	26527	OMIM:252930	Mucopolysaccharidosis type IIIC		86
HP:0002703	HP:0002703	Abnormality of skull ossification	0	HHAT CL E G H	55733	18270	ORPHA:1422	Chondrodysplasia-disorder of sex development syndrome
HP:0002703	HP:0002703	Abnormality of skull ossification	0	IFT43 CL E G H	112752	29669	OMIM:617866	SHORT-RIB THORACIC DYSPLASIA 18 WITH POLYDACTYLY; SRTD18		11
HP:0002703	HP:0002703	Abnormality of skull ossification	0	INTU CL E G H	27152	29239	OMIM:617925	Short-Rib thoracic dysplasia 20 with polydactyly
HP:0002703	HP:0002703	Abnormality of skull ossification	0	LAMA5 CL E G H	3911	6485	OMIM:620076			5
HP:0002703	HP:0002703	Abnormality of skull ossification	0	LBR CL E G H	3930	6518	ORPHA:1426	Greenberg dysplasia		70
HP:0002703	HP:0002703	Abnormality of skull ossification	0	LBR CL E G H	3930	6518	OMIM:215140	Greenberg dysplasia		70
HP:0002703	HP:0002703	Abnormality of skull ossification	0	LMNA CL E G H	4000	6636	ORPHA:1662	Restrictive dermopathy		645
HP:0002703	HP:0002703	Abnormality of skull ossification	0	MPL CL E G H	4352	7217	ORPHA:3319	Congenital amegakaryocytic thrombocytopenia		97
HP:0002703	HP:0002703	Abnormality of skull ossification	0	NAGLU CL E G H	4669	7632	OMIM:252920	Mucopolysaccharidosis type IIIB		72
HP:0002703	HP:0002703	Abnormality of skull ossification	0	NOTCH2 CL E G H	4853	7882	ORPHA:955	Hajdu-Cheney syndrome		138
HP:0002703	HP:0002703	Abnormality of skull ossification	0	OSTM1 CL E G H	28962	21652	ORPHA:85179	Infantile osteopetrosis with neuroaxonal dysplasia		73
HP:0002703	HP:0002703	Abnormality of skull ossification	0	P3H1 CL E G H	64175	19316	OMIM:610915	Osteogenesis imperfecta, type VIII		43
HP:0002703	HP:0002703	Abnormality of skull ossification	0	PHF21A CL E G H	51317	24156	ORPHA:52022	Potocki-Shaffer syndrome		2
HP:0002703	HP:0002703	Abnormality of skull ossification	0	PPIB CL E G H	5479	9255	OMIM:259440	Osteogenesis imperfecta, type IX		39
HP:0002703	HP:0002703	Abnormality of skull ossification	0	RBL2 CL E G H	5934	9894	OMIM:619690	BRUNET-WAGNER NEURODEVELOPMENTAL SYNDROME; BRUWAG
HP:0002703	HP:0002703	Abnormality of skull ossification	0	RUNX2 CL E G H	860	10472	ORPHA:1452	Cleidocranial dysplasia		90
HP:0002703	HP:0002703	Abnormality of skull ossification	0	SEC23A CL E G H	10484	10701	ORPHA:50814	Craniolenticulosutural dysplasia		2
HP:0002703	HP:0002703	Abnormality of skull ossification	0	SGSH CL E G H	6448	10818	OMIM:252900	Mucopolysaccharidosis type IIIA		97
HP:0002703	HP:0002703	Abnormality of skull ossification	0	SLC25A19 CL E G H	60386	14409	ORPHA:99742	Amish lethal microcephaly		36
HP:0002703	HP:0002703	Abnormality of skull ossification	0	SLC25A24 CL E G H	29957	20662	ORPHA:2963	Progeroid syndrome, Petty type
HP:0002703	HP:0002703	Abnormality of skull ossification	0	TAPT1 CL E G H	202018	26887	OMIM:616897	Osteochondrodysplasia, complex lethal, Symoens-Barnes-Gistelinck type		2
HP:0002703	HP:0002703	Abnormality of skull ossification	0	TBCE CL E G H	6905	11582	ORPHA:93324	Autosomal recessive Kenny-Caffey syndrome		52
HP:0002703	HP:0002703	Abnormality of skull ossification	0	TBCE CL E G H	6905	11582	OMIM:244460	Kenny-caffey syndrome, type 1		52
HP:0002703	HP:0002703	Abnormality of skull ossification	0	THPO CL E G H	7066	11795	ORPHA:3319	Congenital amegakaryocytic thrombocytopenia		23
HP:0002703	HP:0002703	Abnormality of skull ossification	0	TRIP11 CL E G H	9321	12305	OMIM:200600	Achondrogenesis, type IA		133
HP:0002703	HP:0002703	Abnormality of skull ossification	0	TXNDC15 CL E G H	79770	20652	OMIM:619879			2
HP:0002703	HP:0002703	Abnormality of skull ossification	0	VAC14 CL E G H	55697	25507	ORPHA:3472	Yunis-Varon syndrome		6
HP:0002703	HP:0002703	Abnormality of skull ossification	0	VCP CL E G H	7415	12666	ORPHA:329475	Spastic paraplegia-Paget disease of bone syndrome		63
HP:0002703	HP:0002703	Abnormality of skull ossification	0	WNT7A CL E G H	7476	12786	OMIM:276820	Ulna and fibula, absence of, with severe limb deficiency		13
HP:0002703	HP:0002703	Abnormality of skull ossification	0	ZMPSTE24 CL E G H	10269	12877	ORPHA:1662	Restrictive dermopathy		83
HP:0002703	HP:0002703	Abnormality of skull ossification	0	ZMPSTE24 CL E G H	10269	12877	OMIM:275210	Restrictive dermopathy, lethal		83
HP:0002703	HP:0004331	Decreased skull ossification	1	ALG9 CL E G H	79796	15672	OMIM:263210	Gillessen-Kaesbach-Nishimura syndrome		93
HP:0002703	HP:0004331	Decreased skull ossification	1	ALPL CL E G H	249	438	OMIM:241500	Hypophosphatasia, infantile		126
HP:0002703	HP:0004331	Decreased skull ossification	1	ALX4 CL E G H	60529	450	ORPHA:52022	Potocki-Shaffer syndrome	HP:0040281 - Very frequent	132
HP:0002703	HP:0004331	Decreased skull ossification	1	ANTXR1 CL E G H	84168	21014	ORPHA:2067	GAPO syndrome	HP:0040283 - Occasional	8
HP:0002703	HP:0004331	Decreased skull ossification	1	BMPER CL E G H	168667	24154	OMIM:608022	DIAPHANOSPONDYLODYSOSTOSIS		78
HP:0002703	HP:0004331	Decreased skull ossification	1	COL1A1 CL E G H	1277	2197	OMIM:166210	Osteogenesis imperfecta, type IIA		373
HP:0002703	HP:0004331	Decreased skull ossification	1	COL1A1 CL E G H	1277	2197	OMIM:259420	Osteogenesis imperfecta, type III		373
HP:0002703	HP:0004331	Decreased skull ossification	1	COL1A2 CL E G H	1278	2198	OMIM:166210	Osteogenesis imperfecta, type IIA		243
HP:0002703	HP:0004331	Decreased skull ossification	1	COL1A2 CL E G H	1278	2198	OMIM:259420	Osteogenesis imperfecta, type III		243
HP:0002703	HP:0004331	Decreased skull ossification	1	COL2A1 CL E G H	1280	2200	OMIM:151210	Platyspondylic lethal skeletal dysplasia, Torrance type		284
HP:0002703	HP:0004331	Decreased skull ossification	1	CREB3L1 CL E G H	90993	18856	OMIM:616229	Osteogenesis imperfecta, type XVI		4
HP:0002703	HP:0004331	Decreased skull ossification	1	CRTAP CL E G H	10491	2379	OMIM:610682	Osteogenesis imperfecta, type VII		124
HP:0002703	HP:0004330	Increased skull ossification	1	CSF1R CL E G H	1436	2433	OMIM:618476	Brain abnormalities, neurodegeneration, and dysosteosclerosis		149
HP:0002703	HP:0004331	Decreased skull ossification	1	EXT2 CL E G H	2132	3513	ORPHA:52022	Potocki-Shaffer syndrome	HP:0040281 - Very frequent	102
HP:0002703	HP:0004331	Decreased skull ossification	1	FAM111A CL E G H	63901	24725	ORPHA:93325	Autosomal dominant Kenny-Caffey syndrome	HP:0040282 - Frequent	8
HP:0002703	HP:0004331	Decreased skull ossification	1	FAM111A CL E G H	63901	24725	OMIM:602361	Gracile bone dysplasia	HP:0040283 - Occasional	8
HP:0002703	HP:0004331	Decreased skull ossification	1	FGFR2 CL E G H	2263	3689	ORPHA:313855	FGFR2-related bent bone dysplasia		175
HP:0002703	HP:0004331	Decreased skull ossification	1	FIG4 CL E G H	9896	16873	OMIM:216340	Yunis-Varon syndrome	.	111
HP:0002703	HP:0004331	Decreased skull ossification	1	FIG4 CL E G H	9896	16873	ORPHA:3472	Yunis-Varon syndrome	HP:0040282 - Frequent	111
HP:0002703	HP:0004331	Decreased skull ossification	1	HDAC6 CL E G H	10013	14064	OMIM:300863	Chondrodysplasia with platyspondyly, distinctive brachydactyly, hydrocephaly, and microphthalmia	.	2
HP:0002703	HP:0004330	Increased skull ossification	1	HGSNAT CL E G H	138050	26527	OMIM:252930	Mucopolysaccharidosis type IIIC		86
HP:0002703	HP:0004330	Increased skull ossification	1	HHAT CL E G H	55733	18270	ORPHA:1422	Chondrodysplasia-disorder of sex development syndrome	HP:0040281 - Very frequent
HP:0002703	HP:0004331	Decreased skull ossification	1	IFT43 CL E G H	112752	29669	OMIM:617866	SHORT-RIB THORACIC DYSPLASIA 18 WITH POLYDACTYLY; SRTD18		11
HP:0002703	HP:0004331	Decreased skull ossification	1	INTU CL E G H	27152	29239	OMIM:617925	Short-Rib thoracic dysplasia 20 with polydactyly
HP:0002703	HP:0004331	Decreased skull ossification	1	LAMA5 CL E G H	3911	6485	OMIM:620076			5
HP:0002703	HP:0004331	Decreased skull ossification	1	LBR CL E G H	3930	6518	OMIM:215140	Greenberg dysplasia		70
HP:0002703	HP:0004331	Decreased skull ossification	1	LBR CL E G H	3930	6518	ORPHA:1426	Greenberg dysplasia	HP:0040282 - Frequent	70
HP:0002703	HP:0004331	Decreased skull ossification	1	LMNA CL E G H	4000	6636	ORPHA:1662	Restrictive dermopathy	HP:0040281 - Very frequent	645
HP:0002703	HP:0004331	Decreased skull ossification	1	MPL CL E G H	4352	7217	ORPHA:3319	Congenital amegakaryocytic thrombocytopenia	HP:0040283 - Occasional	97
HP:0002703	HP:0004330	Increased skull ossification	1	NAGLU CL E G H	4669	7632	OMIM:252920	Mucopolysaccharidosis type IIIB		72
HP:0002703	HP:0004331	Decreased skull ossification	1	NOTCH2 CL E G H	4853	7882	ORPHA:955	Hajdu-Cheney syndrome	HP:0040281 - Very frequent	138
HP:0002703	HP:0004330	Increased skull ossification	1	OSTM1 CL E G H	28962	21652	ORPHA:85179	Infantile osteopetrosis with neuroaxonal dysplasia	HP:0040282 - Frequent	73
HP:0002703	HP:0004331	Decreased skull ossification	1	P3H1 CL E G H	64175	19316	OMIM:610915	Osteogenesis imperfecta, type VIII	.	43
HP:0002703	HP:0004331	Decreased skull ossification	1	PHF21A CL E G H	51317	24156	ORPHA:52022	Potocki-Shaffer syndrome	HP:0040281 - Very frequent	2
HP:0002703	HP:0004331	Decreased skull ossification	1	PPIB CL E G H	5479	9255	OMIM:259440	Osteogenesis imperfecta, type IX		39
HP:0002703	HP:0004330	Increased skull ossification	1	RBL2 CL E G H	5934	9894	OMIM:619690	BRUNET-WAGNER NEURODEVELOPMENTAL SYNDROME; BRUWAG
HP:0002703	HP:0004331	Decreased skull ossification	1	RUNX2 CL E G H	860	10472	ORPHA:1452	Cleidocranial dysplasia	HP:0040282 - Frequent	90
HP:0002703	HP:0004331	Decreased skull ossification	1	SEC23A CL E G H	10484	10701	ORPHA:50814	Craniolenticulosutural dysplasia	HP:0040281 - Very frequent	2
HP:0002703	HP:0004330	Increased skull ossification	1	SGSH CL E G H	6448	10818	OMIM:252900	Mucopolysaccharidosis type IIIA		97
HP:0002703	HP:0004331	Decreased skull ossification	1	SLC25A19 CL E G H	60386	14409	ORPHA:99742	Amish lethal microcephaly	HP:0040283 - Occasional	36
HP:0002703	HP:0004331	Decreased skull ossification	1	SLC25A24 CL E G H	29957	20662	ORPHA:2963	Progeroid syndrome, Petty type	HP:0040281 - Very frequent
HP:0002703	HP:0004331	Decreased skull ossification	1	TAPT1 CL E G H	202018	26887	OMIM:616897	Osteochondrodysplasia, complex lethal, Symoens-Barnes-Gistelinck type		2
HP:0002703	HP:0004331	Decreased skull ossification	1	TBCE CL E G H	6905	11582	ORPHA:93324	Autosomal recessive Kenny-Caffey syndrome	HP:0040282 - Frequent	52
HP:0002703	HP:0004331	Decreased skull ossification	1	TBCE CL E G H	6905	11582	OMIM:244460	Kenny-caffey syndrome, type 1	.	52
HP:0002703	HP:0004331	Decreased skull ossification	1	THPO CL E G H	7066	11795	ORPHA:3319	Congenital amegakaryocytic thrombocytopenia	HP:0040283 - Occasional	23
HP:0002703	HP:0004331	Decreased skull ossification	1	TRIP11 CL E G H	9321	12305	OMIM:200600	Achondrogenesis, type IA	.	133
HP:0002703	HP:0004331	Decreased skull ossification	1	TXNDC15 CL E G H	79770	20652	OMIM:619879			2
HP:0002703	HP:0004331	Decreased skull ossification	1	VAC14 CL E G H	55697	25507	ORPHA:3472	Yunis-Varon syndrome	HP:0040282 - Frequent	6
HP:0002703	HP:0004330	Increased skull ossification	1	VCP CL E G H	7415	12666	ORPHA:329475	Spastic paraplegia-Paget disease of bone syndrome		63
HP:0002703	HP:0004331	Decreased skull ossification	1	WNT7A CL E G H	7476	12786	OMIM:276820	Ulna and fibula, absence of, with severe limb deficiency		13
HP:0002703	HP:0004331	Decreased skull ossification	1	ZMPSTE24 CL E G H	10269	12877	ORPHA:1662	Restrictive dermopathy	HP:0040281 - Very frequent	83
HP:0002703	HP:0004331	Decreased skull ossification	1	ZMPSTE24 CL E G H	10269	12877	OMIM:275210	Restrictive dermopathy, lethal		83
HP:0002703	HP:0005474	Decreased calvarial ossification	2	ALPL CL E G H	249	438	OMIM:241500	Hypophosphatasia, infantile	.	126
HP:0002703	HP:0005474	Decreased calvarial ossification	2	COL1A1 CL E G H	1277	2197	OMIM:166210	Osteogenesis imperfecta, type IIA		373
HP:0002703	HP:0005474	Decreased calvarial ossification	2	COL1A1 CL E G H	1277	2197	OMIM:259420	Osteogenesis imperfecta, type III	.	373
HP:0002703	HP:0005474	Decreased calvarial ossification	2	COL1A2 CL E G H	1278	2198	OMIM:166210	Osteogenesis imperfecta, type IIA		243
HP:0002703	HP:0005474	Decreased calvarial ossification	2	COL1A2 CL E G H	1278	2198	OMIM:259420	Osteogenesis imperfecta, type III	.	243
HP:0002703	HP:0005451	Decreased cranial base ossification	2	COL2A1 CL E G H	1280	2200	OMIM:151210	Platyspondylic lethal skeletal dysplasia, Torrance type	.	284
HP:0002703	HP:0005474	Decreased calvarial ossification	2	CREB3L1 CL E G H	90993	18856	OMIM:616229	Osteogenesis imperfecta, type XVI		4
HP:0002703	HP:0005474	Decreased calvarial ossification	2	CRTAP CL E G H	10491	2379	OMIM:610682	Osteogenesis imperfecta, type VII	.	124
HP:0002703	HP:0005474	Decreased calvarial ossification	2	FGFR2 CL E G H	2263	3689	ORPHA:313855	FGFR2-related bent bone dysplasia	HP:0040281 - Very frequent	175
HP:0002703	HP:0005474	Decreased calvarial ossification	2	FIG4 CL E G H	9896	16873	OMIM:216340	Yunis-Varon syndrome		111
HP:0002703	HP:0000250	Dense calvaria	2	HGSNAT CL E G H	138050	26527	OMIM:252930	Mucopolysaccharidosis type IIIC	.	86
HP:0002703	HP:0005474	Decreased calvarial ossification	2	IFT43 CL E G H	112752	29669	OMIM:617866	SHORT-RIB THORACIC DYSPLASIA 18 WITH POLYDACTYLY; SRTD18		11
HP:0002703	HP:0005474	Decreased calvarial ossification	2	INTU CL E G H	27152	29239	OMIM:617925	Short-Rib thoracic dysplasia 20 with polydactyly
HP:0002703	HP:0005474	Decreased calvarial ossification	2	LAMA5 CL E G H	3911	6485	OMIM:620076			5
HP:0002703	HP:0000250	Dense calvaria	2	NAGLU CL E G H	4669	7632	OMIM:252920	Mucopolysaccharidosis type IIIB	.	72
HP:0002703	HP:0005474	Decreased calvarial ossification	2	P3H1 CL E G H	64175	19316	OMIM:610915	Osteogenesis imperfecta, type VIII		43
HP:0002703	HP:0005474	Decreased calvarial ossification	2	PPIB CL E G H	5479	9255	OMIM:259440	Osteogenesis imperfecta, type IX		39
HP:0002703	HP:0000250	Dense calvaria	2	SGSH CL E G H	6448	10818	OMIM:252900	Mucopolysaccharidosis type IIIA	.	97
HP:0002703	HP:0005474	Decreased calvarial ossification	2	TXNDC15 CL E G H	79770	20652	OMIM:619879			2
HP:0002703	HP:0004563	Increased spinal bone density	2	VCP CL E G H	7415	12666	ORPHA:329475	Spastic paraplegia-Paget disease of bone syndrome	HP:0040281 - Very frequent	63
HP:0002703	HP:0005474	Decreased calvarial ossification	2	WNT7A CL E G H	7476	12786	OMIM:276820	Ulna and fibula, absence of, with severe limb deficiency	.	13
HP:0002703	HP:0005474	Decreased calvarial ossification	2	ZMPSTE24 CL E G H	10269	12877	OMIM:275210	Restrictive dermopathy, lethal	.	83
HP:0002703	HP:0005623	Absent ossification of calvaria	3	COL1A1 CL E G H	1277	2197	OMIM:166210	Osteogenesis imperfecta, type IIA		373
HP:0002703	HP:0005623	Absent ossification of calvaria	3	COL1A2 CL E G H	1278	2198	OMIM:166210	Osteogenesis imperfecta, type IIA		243