Human Phenotype Ontology

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Hello! Guest! Please Login or Register! Clinician Mode

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:
Spinal dysraphism (HP:0010301)

Parent Node:
Spina bifida (HP:0002414)

..Starting node
..Spina bifida occulta (HP:0003298)

Term ID:

3298

Name:

Spina bifida occulta

Synonym:

Definition:

The closed form of spina bifida with incomplete closure of a vertebral body with intact overlying skin.

Comments:

Reference:

HP:0003298

Genes and Diseases:

Child Nodes:

........

Spina bifida occulta at L5 (HP:0004601)

........

Spina bifida occulta at S1 (HP:0004614)

Sister Nodes:

Cervical spina bifida (HP:0005857)

Meningocele (HP:0002435)

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:0003298	HP:0003298	Spina bifida occulta	0	ACTB CL E G H	60	132	ORPHA:64755	Becker nevus syndrome	HP:0040283 - Occasional	72
HP:0003298	HP:0003298	Spina bifida occulta	0	AMER1 CL E G H	139285	26837	OMIM:300373	Osteopathia striata with cranial sclerosis	.	34
HP:0003298	HP:0003298	Spina bifida occulta	0	AMER1 CL E G H	139285	26837	ORPHA:2780	Osteopathia striata-cranial sclerosis syndrome	HP:0040283 - Occasional	34
HP:0003298	HP:0003298	Spina bifida occulta	0	ARID1B CL E G H	57492	18040	OMIM:135900	Coffin-Siris syndrome 1	.	219
HP:0003298	HP:0003298	Spina bifida occulta	0	ATP6V1B2 CL E G H	526	854	ORPHA:79500	DOORS syndrome	HP:0040284 - Very rare	5
HP:0003298	HP:0003298	Spina bifida occulta	0	B3GLCT CL E G H	145173	20207	ORPHA:709	Peters plus syndrome	HP:0040283 - Occasional	36
HP:0003298	HP:0003298	Spina bifida occulta	0	BAZ1B CL E G H	9031	961	ORPHA:904	Williams syndrome	HP:0040283 - Occasional
HP:0003298	HP:0003298	Spina bifida occulta	0	BCL7B CL E G H	9275	1005	ORPHA:904	Williams syndrome	HP:0040283 - Occasional
HP:0003298	HP:0003298	Spina bifida occulta	0	BMP2 CL E G H	650	1069	OMIM:617877	Short stature, facial dysmorphism, and skeletal anomalies with or without cardiac anomalies	.	13
HP:0003298	HP:0003298	Spina bifida occulta	0	BRAF CL E G H	673	1097	ORPHA:500	Noonan syndrome with multiple lentigines	HP:0040283 - Occasional	276
HP:0003298	HP:0003298	Spina bifida occulta	0	BUD23 CL E G H	114049	16405	ORPHA:904	Williams syndrome	HP:0040283 - Occasional
HP:0003298	HP:0003298	Spina bifida occulta	0	CCBE1 CL E G H	147372	29426	OMIM:235510	Hennekam lymphangiectasia-lymphedema syndrome	.	147
HP:0003298	HP:0003298	Spina bifida occulta	0	CCL2 CL E G H	6347	10618	OMIM:182940	Neural tube defects, susceptibility to	.	3
HP:0003298	HP:0003298	Spina bifida occulta	0	CCNQ CL E G H	92002	28434	OMIM:300707	Toe syndactyly, telecanthus, and anogenital and renal malformations	.	7
HP:0003298	HP:0003298	Spina bifida occulta	0	CDK13 CL E G H	8621	1733	OMIM:617360	Congenital heart defects, dysmorphic facial features, and intellectual developmental disorder		8
HP:0003298	HP:0003298	Spina bifida occulta	0	CHN1 CL E G H	1123	1943	ORPHA:233	Duane retraction syndrome	HP:0040283 - Occasional	35
HP:0003298	HP:0003298	Spina bifida occulta	0	CHRNG CL E G H	1146	1967	ORPHA:2990	Autosomal recessive multiple pterygium syndrome	HP:0040283 - Occasional	68
HP:0003298	HP:0003298	Spina bifida occulta	0	CLIP2 CL E G H	7461	2586	ORPHA:904	Williams syndrome	HP:0040283 - Occasional
HP:0003298	HP:0003298	Spina bifida occulta	0	COL18A1 CL E G H	80781	2195	OMIM:267750	Knobloch syndrome 1		177
HP:0003298	HP:0003298	Spina bifida occulta	0	COLEC10 CL E G H	10584	2220	ORPHA:293843	3MC syndrome	HP:0040282 - Frequent	3
HP:0003298	HP:0003298	Spina bifida occulta	0	COLEC11 CL E G H	78989	17213	ORPHA:293843	3MC syndrome	HP:0040282 - Frequent	9
HP:0003298	HP:0003298	Spina bifida occulta	0	CREBBP CL E G H	1387	2348	OMIM:180849	Rubinstein-Taybi syndrome 1		291
HP:0003298	HP:0003298	Spina bifida occulta	0	CUL7 CL E G H	9820	21024	OMIM:273750	3-M syndrome 1	.	127
HP:0003298	HP:0003298	Spina bifida occulta	0	DACT1 CL E G H	51339	17748	OMIM:617466	Townes-Brocks syndrome 2	.	2
HP:0003298	HP:0003298	Spina bifida occulta	0	DARS1 CL E G H	1615	2678	OMIM:615281	HYPOMYELINATION WITH BRAINSTEM AND SPINAL CORD INVOLVEMENT AND LEG SPASTICITY; HBSL
HP:0003298	HP:0003298	Spina bifida occulta	0	DLL3 CL E G H	10683	2909	ORPHA:2311	Autosomal recessive spondylocostal dysostosis	HP:0040283 - Occasional	45
HP:0003298	HP:0003298	Spina bifida occulta	0	DNAJC30 CL E G H	84277	16410	ORPHA:904	Williams syndrome	HP:0040283 - Occasional
HP:0003298	HP:0003298	Spina bifida occulta	0	EIF4H CL E G H	7458	12741	ORPHA:904	Williams syndrome	HP:0040283 - Occasional
HP:0003298	HP:0003298	Spina bifida occulta	0	ELN CL E G H	2006	3327	ORPHA:904	Williams syndrome	HP:0040283 - Occasional	172
HP:0003298	HP:0003298	Spina bifida occulta	0	EP300 CL E G H	2033	3373	OMIM:180849	Rubinstein-Taybi syndrome 1		250
HP:0003298	HP:0003298	Spina bifida occulta	0	FIBP CL E G H	9158	3705	ORPHA:500095	Tall stature-intellectual disability-renal anomalies syndrome	HP:0040283 - Occasional	2
HP:0003298	HP:0003298	Spina bifida occulta	0	FKBP6 CL E G H	8468	3722	ORPHA:904	Williams syndrome	HP:0040283 - Occasional
HP:0003298	HP:0003298	Spina bifida occulta	0	FLNA CL E G H	2316	3754	ORPHA:1826	Frontometaphyseal dysplasia	HP:0040283 - Occasional	493
HP:0003298	HP:0003298	Spina bifida occulta	0	FLNB CL E G H	2317	3755	OMIM:150250	Larsen syndrome	.	233
HP:0003298	HP:0003298	Spina bifida occulta	0	FUZ CL E G H	80199	26219	OMIM:182940	Neural tube defects, susceptibility to	.	3
HP:0003298	HP:0003298	Spina bifida occulta	0	GTF2I CL E G H	2969	4659	ORPHA:904	Williams syndrome	HP:0040283 - Occasional	1
HP:0003298	HP:0003298	Spina bifida occulta	0	GTF2IRD1 CL E G H	9569	4661	ORPHA:904	Williams syndrome	HP:0040283 - Occasional	1
HP:0003298	HP:0003298	Spina bifida occulta	0	GTF2IRD2 CL E G H	84163	30775	ORPHA:904	Williams syndrome	HP:0040283 - Occasional	1
HP:0003298	HP:0003298	Spina bifida occulta	0	HES7 CL E G H	84667	15977	ORPHA:2311	Autosomal recessive spondylocostal dysostosis	HP:0040283 - Occasional	10
HP:0003298	HP:0003298	Spina bifida occulta	0	HES7 CL E G H	84667	15977	OMIM:613686	Spondylocostal dysostosis 4, autosomal recessive	.	10
HP:0003298	HP:0003298	Spina bifida occulta	0	HMX1 CL E G H	3166	5017	OMIM:612109	Oculoauricular syndrome		2
HP:0003298	HP:0003298	Spina bifida occulta	0	IKBKG CL E G H	8517	5961	ORPHA:464	Incontinentia pigmenti	HP:0040283 - Occasional	52
HP:0003298	HP:0003298	Spina bifida occulta	0	IRF6 CL E G H	3664	6121	OMIM:119500	Popliteal pterygium syndrome	.	99
HP:0003298	HP:0003298	Spina bifida occulta	0	KCNH1 CL E G H	3756	6250	OMIM:135500	Zimmermann-Laband syndrome 1	.	13
HP:0003298	HP:0003298	Spina bifida occulta	0	LFNG CL E G H	3955	6560	ORPHA:2311	Autosomal recessive spondylocostal dysostosis	HP:0040283 - Occasional	13
HP:0003298	HP:0003298	Spina bifida occulta	0	LIG4 CL E G H	3981	6601	ORPHA:235	Dubowitz syndrome	HP:0040283 - Occasional	88
HP:0003298	HP:0003298	Spina bifida occulta	0	LIMK1 CL E G H	3984	6613	ORPHA:904	Williams syndrome	HP:0040283 - Occasional
HP:0003298	HP:0003298	Spina bifida occulta	0	MAFB CL E G H	9935	6408	ORPHA:233	Duane retraction syndrome	HP:0040283 - Occasional	63
HP:0003298	HP:0003298	Spina bifida occulta	0	MAP3K7 CL E G H	6885	6859	ORPHA:1826	Frontometaphyseal dysplasia	HP:0040283 - Occasional	11
HP:0003298	HP:0003298	Spina bifida occulta	0	MASP1 CL E G H	5648	6901	ORPHA:293843	3MC syndrome	HP:0040282 - Frequent	21
HP:0003298	HP:0003298	Spina bifida occulta	0	MASP1 CL E G H	5648	6901	OMIM:257920	3mc syndrome 1	.	21
HP:0003298	HP:0003298	Spina bifida occulta	0	MESP2 CL E G H	145873	29659	ORPHA:2311	Autosomal recessive spondylocostal dysostosis	HP:0040283 - Occasional	45
HP:0003298	HP:0003298	Spina bifida occulta	0	METTL27 CL E G H	155368	19068	ORPHA:904	Williams syndrome	HP:0040283 - Occasional	1
HP:0003298	HP:0003298	Spina bifida occulta	0	MLXIPL CL E G H	51085	12744	ORPHA:904	Williams syndrome	HP:0040283 - Occasional	1
HP:0003298	HP:0003298	Spina bifida occulta	0	MYH3 CL E G H	4621	7573	OMIM:193700	Arthrogryposis, distal, type 2A	.	166
HP:0003298	HP:0003298	Spina bifida occulta	0	MYH3 CL E G H	4621	7573	ORPHA:2990	Autosomal recessive multiple pterygium syndrome	HP:0040283 - Occasional	166
HP:0003298	HP:0003298	Spina bifida occulta	0	NCF1 CL E G H	653361	7660	ORPHA:904	Williams syndrome	HP:0040283 - Occasional	13
HP:0003298	HP:0003298	Spina bifida occulta	0	NEK9 CL E G H	91754	18591	ORPHA:64754	Nevus comedonicus syndrome	HP:0040283 - Occasional	9
HP:0003298	HP:0003298	Spina bifida occulta	0	NOTCH2NLC CL E G H	100996717	53924	ORPHA:2289	Neuronal intranuclear inclusion disease	HP:0040282 - Frequent
HP:0003298	HP:0003298	Spina bifida occulta	0	NSUN2 CL E G H	54888	25994	ORPHA:235	Dubowitz syndrome	HP:0040283 - Occasional	84
HP:0003298	HP:0003298	Spina bifida occulta	0	POLA1 CL E G H	5422	9173	OMIM:301030	Van esch-o'driscoll syndrome	.	2
HP:0003298	HP:0003298	Spina bifida occulta	0	PORCN CL E G H	64840	17652	OMIM:305600	Focal dermal hypoplasia	.	20
HP:0003298	HP:0003298	Spina bifida occulta	0	PTPN11 CL E G H	5781	9644	OMIM:151100	Leopard syndrome 1	.	291
HP:0003298	HP:0003298	Spina bifida occulta	0	PTPN11 CL E G H	5781	9644	ORPHA:500	Noonan syndrome with multiple lentigines	HP:0040283 - Occasional	291
HP:0003298	HP:0003298	Spina bifida occulta	0	PUF60 CL E G H	22827	17042	ORPHA:508488	8q24.3 microdeletion syndrome	HP:0040283 - Occasional	19
HP:0003298	HP:0003298	Spina bifida occulta	0	RAB23 CL E G H	51715	14263	OMIM:201000	Carpenter syndrome 1	.	31
HP:0003298	HP:0003298	Spina bifida occulta	0	RAF1 CL E G H	5894	9829	ORPHA:500	Noonan syndrome with multiple lentigines	HP:0040283 - Occasional	212
HP:0003298	HP:0003298	Spina bifida occulta	0	RECQL4 CL E G H	9401	9949	OMIM:218600	Baller-Gerold syndrome	.	445
HP:0003298	HP:0003298	Spina bifida occulta	0	RFC2 CL E G H	5982	9970	ORPHA:904	Williams syndrome	HP:0040283 - Occasional
HP:0003298	HP:0003298	Spina bifida occulta	0	RIPPLY2 CL E G H	134701	21390	ORPHA:2311	Autosomal recessive spondylocostal dysostosis	HP:0040283 - Occasional	3
HP:0003298	HP:0003298	Spina bifida occulta	0	RORA CL E G H	6095	10258	OMIM:618060	INTELLECTUAL DEVELOPMENTAL DISORDER WITH OR WITHOUT EPILEPSY OR CEREBELLAR ATAXIA; IDDECA		1
HP:0003298	HP:0003298	Spina bifida occulta	0	RUNX2 CL E G H	860	10472	ORPHA:1452	Cleidocranial dysplasia	HP:0040282 - Frequent	90
HP:0003298	HP:0003298	Spina bifida occulta	0	SALL4 CL E G H	57167	15924	ORPHA:233	Duane retraction syndrome	HP:0040283 - Occasional	86
HP:0003298	HP:0003298	Spina bifida occulta	0	SALL4 CL E G H	57167	15924	OMIM:607323	Duane-Radial ray syndrome	.	86
HP:0003298	HP:0003298	Spina bifida occulta	0	STX1A CL E G H	6804	11433	ORPHA:904	Williams syndrome	HP:0040283 - Occasional
HP:0003298	HP:0003298	Spina bifida occulta	0	TBC1D24 CL E G H	57465	29203	ORPHA:79500	DOORS syndrome	HP:0040284 - Very rare	271
HP:0003298	HP:0003298	Spina bifida occulta	0	TBL2 CL E G H	26608	11586	ORPHA:904	Williams syndrome	HP:0040283 - Occasional
HP:0003298	HP:0003298	Spina bifida occulta	0	TBX6 CL E G H	6911	11605	ORPHA:1797	Autosomal dominant spondylocostal dysostosis	HP:0040283 - Occasional	19
HP:0003298	HP:0003298	Spina bifida occulta	0	TBXT CL E G H	6862	11515	OMIM:182940	Neural tube defects, susceptibility to	.
HP:0003298	HP:0003298	Spina bifida occulta	0	TMEM270 CL E G H	135886	23018	ORPHA:904	Williams syndrome	HP:0040283 - Occasional
HP:0003298	HP:0003298	Spina bifida occulta	0	TNXB CL E G H	7148	11976	ORPHA:230839	Classical-like Ehlers-Danlos syndrome type 1	HP:0040283 - Occasional	134
HP:0003298	HP:0003298	Spina bifida occulta	0	VANGL1 CL E G H	81839	15512	OMIM:182940	Neural tube defects, susceptibility to	.	111
HP:0003298	HP:0003298	Spina bifida occulta	0	VANGL2 CL E G H	57216	15511	OMIM:182940	Neural tube defects, susceptibility to	.	2
HP:0003298	HP:0003298	Spina bifida occulta	0	VPS37D CL E G H	155382	18287	ORPHA:904	Williams syndrome	HP:0040283 - Occasional
HP:0003298	HP:0003298	Spina bifida occulta	0	WBP11 CL E G H	51729	16461	OMIM:619227	VERTEBRAL, CARDIAC, TRACHEOESOPHAGEAL, RENAL, AND LIMB DEFECTS; VCTERL
HP:0003298	HP:0003298	Spina bifida occulta	0	ZIC1 CL E G H	7545	12872	OMIM:616602	Craniosynostosis 6	HP:0040283 - Occasional	5
HP:0003298	HP:0003298	Spina bifida occulta	0	ZIC1 CL E G H	7545	12872	OMIM:618736	STRUCTURAL BRAIN ANOMALIES WITH IMPAIRED INTELLECTUAL DEVELOPMENT AND CRANIOSYNOSTOSIS; BAIDCS		5
HP:0003298	HP:0004614	Spina bifida occulta at S1	1	CL E G H
HP:0003298	HP:0004601	Spina bifida occulta at L5	1	CL E G H

Genes (80) :ACTB AMER1 ARID1B ATP6V1B2 B3GLCT BAZ1B BCL7B BMP2 BRAF BUD23 CCBE1 CCL2 CCNQ CDK13 CHN1 CHRNG CLIP2 COL18A1 COLEC10 COLEC11 CREBBP CUL7 DACT1 DARS1 DLL3 DNAJC30 EIF4H ELN EP300 FIBP FKBP6 FLNA FLNB FUZ GTF2I GTF2IRD1 GTF2IRD2 HES7 HMX1 IKBKG IRF6 KCNH1 LFNG LIG4 LIMK1 MAFB MAP3K7 MASP1 MESP2 METTL27 MLXIPL MYH3 NCF1 NEK9 NOTCH2NLC NSUN2 POLA1 PORCN PTPN11 PUF60 RAB23 RAF1 RECQL4 RFC2 RIPPLY2 RORA RUNX2 SALL4 STX1A TBC1D24 TBL2 TBX6 TBXT TMEM270 TNXB VANGL1 VANGL2 VPS37D WBP11 ZIC1

Diseases (49) :ORPHA:64755 OMIM:300373 ORPHA:2780 OMIM:135900 ORPHA:79500 ORPHA:709 ORPHA:904 OMIM:617877 ORPHA:500 OMIM:235510 OMIM:182940 OMIM:300707 OMIM:617360 ORPHA:233 ORPHA:2990 OMIM:267750 ORPHA:293843 OMIM:180849 OMIM:273750 OMIM:617466 OMIM:615281 ORPHA:2311 ORPHA:500095 ORPHA:1826 OMIM:150250 OMIM:613686 OMIM:612109 ORPHA:464 OMIM:119500 OMIM:135500 ORPHA:235 OMIM:257920 OMIM:193700 ORPHA:64754 ORPHA:2289 OMIM:301030 OMIM:305600 OMIM:151100 ORPHA:508488 OMIM:201000 OMIM:218600 OMIM:618060 ORPHA:1452 OMIM:607323 ORPHA:1797 ORPHA:230839 OMIM:619227 OMIM:616602 OMIM:618736

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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