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:
Abdominal wall defect (HP:0010866)

Grandparent Node:
Hernia (HP:0100790)

Parent Node:
Hernia of the abdominal wall (HP:0004299)

..Starting node
..Omphalocele (HP:0001539)

Term ID:

1539

Name:

Omphalocele

Synonym:

Exomphalos; Omphalocoele

Definition:

A midline anterior incomplete closure of the abdominal wall in which there is herniation of the abdominal viscera into the base of the abdominal cord.

Comments:

Reference:

HP:0001539

Genes and Diseases:

Child Nodes:

Sister Nodes:

Femoral hernia (HP:0100541)

Incisional hernia (HP:0004872)

Inguinal hernia (HP:0000023)

Umbilical hernia (HP:0001537)

Ventral hernia (HP:0002933)

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:0001539	HP:0001539	Omphalocele	0	ACTG2 CL E G H	72	145	ORPHA:2241	Megacystis-microcolon-intestinal hypoperistalsis syndrome	HP:0040283 - Occasional	23
HP:0001539	HP:0001539	Omphalocele	0	ALG9 CL E G H	79796	15672	ORPHA:79328	ALG9-CDG	HP:0040283 - Occasional	93
HP:0001539	HP:0001539	Omphalocele	0	ALG9 CL E G H	79796	15672	OMIM:263210	Gillessen-Kaesbach-Nishimura syndrome		93
HP:0001539	HP:0001539	Omphalocele	0	AMER1 CL E G H	139285	26837	OMIM:300373	Osteopathia striata with cranial sclerosis	HP:0040284 - Very rare	34
HP:0001539	HP:0001539	Omphalocele	0	AR CL E G H	367	644	ORPHA:95706	Non-syndromic posterior hypospadias	HP:0040283 - Occasional	125
HP:0001539	HP:0001539	Omphalocele	0	BHLHA9 CL E G H	727857	35126	ORPHA:3329	Tibial aplasia-ectrodactyly syndrome	HP:0040283 - Occasional	4
HP:0001539	HP:0001539	Omphalocele	0	CD96 CL E G H	10225	16892	ORPHA:1308	C syndrome	HP:0040283 - Occasional	83
HP:0001539	HP:0001539	Omphalocele	0	CD96 CL E G H	10225	16892	OMIM:211750	C syndrome	.	83
HP:0001539	HP:0001539	Omphalocele	0	CDKN1C CL E G H	1028	1786	OMIM:130650	Beckwith-Wiedemann syndrome	.	114
HP:0001539	HP:0001539	Omphalocele	0	CEP120 CL E G H	153241	26690	OMIM:616300	Short-Rib thoracic dysplasia 13 with or without polydactyly	.	7
HP:0001539	HP:0001539	Omphalocele	0	CHD7 CL E G H	55636	20626	OMIM:214800	Charge syndrome	.	515
HP:0001539	HP:0001539	Omphalocele	0	CHUK CL E G H	1147	1974	OMIM:613630	Fetal encasement syndrome		3
HP:0001539	HP:0001539	Omphalocele	0	COL11A1 CL E G H	1301	2186	ORPHA:2021	Fibrochondrogenesis	HP:0040283 - Occasional	215
HP:0001539	HP:0001539	Omphalocele	0	COL11A1 CL E G H	1301	2186	OMIM:228520	Fibrochondrogenesis 1	.	215
HP:0001539	HP:0001539	Omphalocele	0	COL11A2 CL E G H	1302	2187	ORPHA:2021	Fibrochondrogenesis	HP:0040283 - Occasional	222
HP:0001539	HP:0001539	Omphalocele	0	DACT1 CL E G H	51339	17748	ORPHA:63260	Craniorachischisis	HP:0040283 - Occasional	2
HP:0001539	HP:0001539	Omphalocele	0	DLK1 CL E G H	8788	2907	ORPHA:254534	Kagami-Ogata syndrome due to maternal 14q32.2 hypermethylation	HP:0040283 - Occasional	1
HP:0001539	HP:0001539	Omphalocele	0	DLK1 CL E G H	8788	2907	ORPHA:254528	Kagami-Ogata syndrome due to maternal 14q32.2 microdeletion	HP:0040283 - Occasional	1
HP:0001539	HP:0001539	Omphalocele	0	DLK1 CL E G H	8788	2907	ORPHA:96334	Kagami-Ogata syndrome due to paternal uniparental disomy of chromosome 14	HP:0040283 - Occasional	1
HP:0001539	HP:0001539	Omphalocele	0	DVL3 CL E G H	1857	3087	OMIM:616894	ROBINOW SYNDROME, AUTOSOMAL DOMINANT 3; DRS3		5
HP:0001539	HP:0001539	Omphalocele	0	DYNC2H1 CL E G H	79659	2962	ORPHA:93271	Short rib-polydactyly syndrome, Verma-Naumoff type	HP:0040283 - Occasional	304
HP:0001539	HP:0001539	Omphalocele	0	DYNC2I1 CL E G H	55112	21862	ORPHA:93271	Short rib-polydactyly syndrome, Verma-Naumoff type	HP:0040283 - Occasional
HP:0001539	HP:0001539	Omphalocele	0	DYNC2I2 CL E G H	89891	28296	ORPHA:93271	Short rib-polydactyly syndrome, Verma-Naumoff type	HP:0040283 - Occasional
HP:0001539	HP:0001539	Omphalocele	0	FGFR1 CL E G H	2260	3688	ORPHA:3366	Isolated trigonocephaly	HP:0040283 - Occasional	172
HP:0001539	HP:0001539	Omphalocele	0	FGFR1 CL E G H	2260	3688	OMIM:190440	Trigonocephaly 1	.	172
HP:0001539	HP:0001539	Omphalocele	0	FLNA CL E G H	2316	3754	ORPHA:2484	Melnick-Needles syndrome	HP:0040283 - Occasional	493
HP:0001539	HP:0001539	Omphalocele	0	FLNA CL E G H	2316	3754	OMIM:309350	Melnick-Needles syndrome	.	493
HP:0001539	HP:0001539	Omphalocele	0	FLNA CL E G H	2316	3754	ORPHA:90652	Otopalatodigital syndrome type 2	HP:0040282 - Frequent	493
HP:0001539	HP:0001539	Omphalocele	0	FLNA CL E G H	2316	3754	OMIM:311300	Otopalatodigital syndrome, type I	.	493
HP:0001539	HP:0001539	Omphalocele	0	FLNA CL E G H	2316	3754	OMIM:304120	Otopalatodigital syndrome, type II	.	493
HP:0001539	HP:0001539	Omphalocele	0	FLNB CL E G H	2317	3755	ORPHA:1263	Boomerang dysplasia	HP:0040282 - Frequent	233
HP:0001539	HP:0001539	Omphalocele	0	FOXF1 CL E G H	2294	3809	OMIM:265380	Alveolar capillary dysplasia with misalignment of pulmonary veins		61
HP:0001539	HP:0001539	Omphalocele	0	FRAS1 CL E G H	80144	19185	ORPHA:2052	Fraser syndrome	HP:0040283 - Occasional	353
HP:0001539	HP:0001539	Omphalocele	0	FREM1 CL E G H	158326	23399	ORPHA:3366	Isolated trigonocephaly	HP:0040283 - Occasional	198
HP:0001539	HP:0001539	Omphalocele	0	FREM1 CL E G H	158326	23399	OMIM:248450	Manitoba oculotrichoanal syndrome	.	198
HP:0001539	HP:0001539	Omphalocele	0	FREM2 CL E G H	341640	25396	ORPHA:2052	Fraser syndrome	HP:0040283 - Occasional	263
HP:0001539	HP:0001539	Omphalocele	0	GAD1 CL E G H	2571	4092	OMIM:619124	DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 89; DEE89		44
HP:0001539	HP:0001539	Omphalocele	0	GPC3 CL E G H	2719	4451	ORPHA:373	Simpson-Golabi-Behmel syndrome	HP:0040282 - Frequent	73
HP:0001539	HP:0001539	Omphalocele	0	GPC4 CL E G H	2239	4452	ORPHA:373	Simpson-Golabi-Behmel syndrome	HP:0040282 - Frequent
HP:0001539	HP:0001539	Omphalocele	0	GRIP1 CL E G H	23426	18708	ORPHA:2052	Fraser syndrome	HP:0040283 - Occasional	80
HP:0001539	HP:0001539	Omphalocele	0	H19-ICR CL E G H	105259599		OMIM:130650	Beckwith-Wiedemann syndrome	.
HP:0001539	HP:0001539	Omphalocele	0	HIC1 CL E G H	3090	4909	ORPHA:531	Miller-Dieker syndrome	HP:0040283 - Occasional
HP:0001539	HP:0001539	Omphalocele	0	HOXD13 CL E G H	3239	5136	ORPHA:887	VACTERL/VATER association	HP:0040283 - Occasional	25
HP:0001539	HP:0001539	Omphalocele	0	HYLS1 CL E G H	219844	26558	OMIM:236680	Hydrolethalus syndrome 1	.	31
HP:0001539	HP:0001539	Omphalocele	0	IFT80 CL E G H	57560	29262	ORPHA:93271	Short rib-polydactyly syndrome, Verma-Naumoff type	HP:0040283 - Occasional	65
HP:0001539	HP:0001539	Omphalocele	0	IFT81 CL E G H	28981	14313	OMIM:617895	Short-Rib thoracic dysplasia 19 with or without polydactyly	.	2
HP:0001539	HP:0001539	Omphalocele	0	IGF2 CL E G H	3481	5466	OMIM:130650	Beckwith-Wiedemann syndrome	.	9
HP:0001539	HP:0001539	Omphalocele	0	ISL1 CL E G H	3670	6132	ORPHA:93930	Bladder exstrophy	HP:0040283 - Occasional	2
HP:0001539	HP:0001539	Omphalocele	0	KCNQ1 CL E G H	3784	6294	OMIM:130650	Beckwith-Wiedemann syndrome	.	730
HP:0001539	HP:0001539	Omphalocele	0	KCNQ1OT1 CL E G H	10984	6295	OMIM:130650	Beckwith-Wiedemann syndrome	.	1
HP:0001539	HP:0001539	Omphalocele	0	LMOD1 CL E G H	25802	6647	ORPHA:2241	Megacystis-microcolon-intestinal hypoperistalsis syndrome	HP:0040283 - Occasional
HP:0001539	HP:0001539	Omphalocele	0	LONP1 CL E G H	9361	9479	OMIM:600373	CODAS syndrome		8
HP:0001539	HP:0001539	Omphalocele	0	LRP2 CL E G H	4036	6694	OMIM:222448	Donnai-Barrow syndrome		289
HP:0001539	HP:0001539	Omphalocele	0	LRP2 CL E G H	4036	6694	ORPHA:2143	Donnai-Barrow syndrome	HP:0040282 - Frequent	289
HP:0001539	HP:0001539	Omphalocele	0	MAMLD1 CL E G H	10046	2568	ORPHA:95706	Non-syndromic posterior hypospadias	HP:0040283 - Occasional	5
HP:0001539	HP:0001539	Omphalocele	0	MASP1 CL E G H	5648	6901	OMIM:257920	3mc syndrome 1	.	21
HP:0001539	HP:0001539	Omphalocele	0	MBTPS2 CL E G H	51360	15455	ORPHA:2273	Ichthyosis follicularis-alopecia-photophobia syndrome	HP:0040283 - Occasional	22
HP:0001539	HP:0001539	Omphalocele	0	MEG3 CL E G H	55384	14575	ORPHA:254534	Kagami-Ogata syndrome due to maternal 14q32.2 hypermethylation	HP:0040283 - Occasional	1
HP:0001539	HP:0001539	Omphalocele	0	MEG3 CL E G H	55384	14575	ORPHA:254528	Kagami-Ogata syndrome due to maternal 14q32.2 microdeletion	HP:0040283 - Occasional	1
HP:0001539	HP:0001539	Omphalocele	0	MEG3 CL E G H	55384	14575	ORPHA:96334	Kagami-Ogata syndrome due to paternal uniparental disomy of chromosome 14	HP:0040283 - Occasional	1
HP:0001539	HP:0001539	Omphalocele	0	MID1 CL E G H	4281	7095	ORPHA:2745	Opitz GBBB syndrome	HP:0040283 - Occasional	57
HP:0001539	HP:0001539	Omphalocele	0	MKS1 CL E G H	54903	7121	OMIM:249000	Meckel syndrome 1	.	127
HP:0001539	HP:0001539	Omphalocele	0	MMP14 CL E G H	4323	7160	ORPHA:371428	Multicentric osteolysis-nodulosis-arthropathy spectrum	HP:0040283 - Occasional	2
HP:0001539	HP:0001539	Omphalocele	0	MMP2 CL E G H	4313	7166	ORPHA:371428	Multicentric osteolysis-nodulosis-arthropathy spectrum	HP:0040283 - Occasional	64
HP:0001539	HP:0001539	Omphalocele	0	MTHFR CL E G H	4524	7436	ORPHA:563609	Isolated anencephaly	HP:0040283 - Occasional	183
HP:0001539	HP:0001539	Omphalocele	0	MYH11 CL E G H	4629	7569	ORPHA:2241	Megacystis-microcolon-intestinal hypoperistalsis syndrome	HP:0040283 - Occasional	418
HP:0001539	HP:0001539	Omphalocele	0	MYLK CL E G H	4638	7590	ORPHA:2241	Megacystis-microcolon-intestinal hypoperistalsis syndrome	HP:0040283 - Occasional	326
HP:0001539	HP:0001539	Omphalocele	0	NEK9 CL E G H	91754	18591	OMIM:617022	Lethal congenital contracture syndrome 10	.	9
HP:0001539	HP:0001539	Omphalocele	0	NFIX CL E G H	4784	7788	OMIM:602535	Marshall-Smith syndrome	.	40
HP:0001539	HP:0001539	Omphalocele	0	NXN CL E G H	64359	18008	OMIM:618529	Robinow syndrome, autosomal recessive 2	.	2
HP:0001539	HP:0001539	Omphalocele	0	PAFAH1B1 CL E G H	5048	8574	ORPHA:531	Miller-Dieker syndrome	HP:0040283 - Occasional	231
HP:0001539	HP:0001539	Omphalocele	0	PI4KA CL E G H	5297	8983	ORPHA:436252	Combined immunodeficiency-enteropathy spectrum	HP:0040284 - Very rare	11
HP:0001539	HP:0001539	Omphalocele	0	PIGN CL E G H	23556	8967	ORPHA:2059	Fryns syndrome	HP:0040283 - Occasional	37
HP:0001539	HP:0001539	Omphalocele	0	PORCN CL E G H	64840	17652	ORPHA:2092	Focal dermal hypoplasia	HP:0040283 - Occasional	20
HP:0001539	HP:0001539	Omphalocele	0	PORCN CL E G H	64840	17652	OMIM:305600	Focal dermal hypoplasia	.	20
HP:0001539	HP:0001539	Omphalocele	0	PPP1R12A CL E G H	4659	7618	OMIM:618820	GENITOURINARY AND/OR BRAIN MALFORMATION SYNDROME; GUBS
HP:0001539	HP:0001539	Omphalocele	0	PPP2R3C CL E G H	55012	17485	OMIM:618419	Gonadal dysgenesis, dysmorphic facies, retinal dystrophy, and myopathy	HP:0040284 - Very rare
HP:0001539	HP:0001539	Omphalocele	0	PTCH1 CL E G H	5727	9585	OMIM:610828	Holoprosencephaly 7		665
HP:0001539	HP:0001539	Omphalocele	0	RAB23 CL E G H	51715	14263	OMIM:201000	Carpenter syndrome 1		31
HP:0001539	HP:0001539	Omphalocele	0	RIPK4 CL E G H	54101	496	OMIM:263650	Popliteal pterygium syndrome, Bartsocas-Papas type 1		69
HP:0001539	HP:0001539	Omphalocele	0	RTL1 CL E G H	388015	14665	ORPHA:254534	Kagami-Ogata syndrome due to maternal 14q32.2 hypermethylation	HP:0040283 - Occasional
HP:0001539	HP:0001539	Omphalocele	0	RTL1 CL E G H	388015	14665	ORPHA:254528	Kagami-Ogata syndrome due to maternal 14q32.2 microdeletion	HP:0040283 - Occasional
HP:0001539	HP:0001539	Omphalocele	0	RTL1 CL E G H	388015	14665	ORPHA:96334	Kagami-Ogata syndrome due to paternal uniparental disomy of chromosome 14	HP:0040283 - Occasional
HP:0001539	HP:0001539	Omphalocele	0	SPECC1L CL E G H	23384	29022	OMIM:145420	Hypertelorism, Teebi type	.	6
HP:0001539	HP:0001539	Omphalocele	0	SPECC1L CL E G H	23384	29022	ORPHA:1519	SPECC1L-related hypertelorism syndrome	HP:0040283 - Occasional	6
HP:0001539	HP:0001539	Omphalocele	0	THRA CL E G H	7067	11796	OMIM:614450	Hypothyroidism, congenital, nongoitrous, 6	.	9
HP:0001539	HP:0001539	Omphalocele	0	TMEM216 CL E G H	51259	25018	OMIM:603194	Meckel syndrome, type 2		45
HP:0001539	HP:0001539	Omphalocele	0	TMEM94 CL E G H	9772	28983	OMIM:618316	Intellectual developmental disorder with cardiac defects and dysmorphic facies		1
HP:0001539	HP:0001539	Omphalocele	0	TP63 CL E G H	8626	15979	ORPHA:93930	Bladder exstrophy	HP:0040283 - Occasional	140
HP:0001539	HP:0001539	Omphalocele	0	TRRAP CL E G H	8295	12347	OMIM:618454	Developmental delay with or without dysmorphic facies and autism		2
HP:0001539	HP:0001539	Omphalocele	0	TSHB CL E G H	7252	12372	OMIM:275100	Hypothyroidism, congenital, nongoitrous, 4	.	9
HP:0001539	HP:0001539	Omphalocele	0	TTC7A CL E G H	57217	19750	ORPHA:436252	Combined immunodeficiency-enteropathy spectrum	HP:0040284 - Very rare	26
HP:0001539	HP:0001539	Omphalocele	0	TTC7A CL E G H	57217	19750	OMIM:243150	Gastrointestinal defects and immunodeficiency syndrome	HP:0040283 - Occasional	26
HP:0001539	HP:0001539	Omphalocele	0	TWIST2 CL E G H	117581	20670	ORPHA:920	Ablepharon macrostomia syndrome	HP:0040283 - Occasional	7
HP:0001539	HP:0001539	Omphalocele	0	TWIST2 CL E G H	117581	20670	OMIM:200110	Ablepharon-Macrostomia syndrome		7
HP:0001539	HP:0001539	Omphalocele	0	VANGL2 CL E G H	57216	15511	ORPHA:563609	Isolated anencephaly	HP:0040283 - Occasional	2
HP:0001539	HP:0001539	Omphalocele	0	WDR35 CL E G H	57539	29250	ORPHA:93271	Short rib-polydactyly syndrome, Verma-Naumoff type	HP:0040283 - Occasional	136
HP:0001539	HP:0001539	Omphalocele	0	YWHAE CL E G H	7531	12851	ORPHA:531	Miller-Dieker syndrome	HP:0040283 - Occasional	14
HP:0001539	HP:0001539	Omphalocele	0	ZIC3 CL E G H	7547	12874	OMIM:306955	Heterotaxy, visceral, 1, X-linked		39

Genes (79) :ACTG2 ALG9 AMER1 AR BHLHA9 CD96 CDKN1C CEP120 CHD7 CHUK COL11A1 COL11A2 DACT1 DLK1 DVL3 DYNC2H1 DYNC2I1 DYNC2I2 FGFR1 FLNA FLNB FOXF1 FRAS1 FREM1 FREM2 GAD1 GPC3 GPC4 GRIP1 H19-ICR HIC1 HOXD13 HYLS1 IFT80 IFT81 IGF2 ISL1 KCNQ1 KCNQ1OT1 LMOD1 LONP1 LRP2 MAMLD1 MASP1 MBTPS2 MEG3 MID1 MKS1 MMP14 MMP2 MTHFR MYH11 MYLK NEK9 NFIX NXN PAFAH1B1 PI4KA PIGN PORCN PPP1R12A PPP2R3C PTCH1 RAB23 RIPK4 RTL1 SPECC1L THRA TMEM216 TMEM94 TP63 TRRAP TSHB TTC7A TWIST2 VANGL2 WDR35 YWHAE ZIC3

Diseases (70) :ORPHA:2241 ORPHA:79328 OMIM:263210 OMIM:300373 ORPHA:95706 ORPHA:3329 ORPHA:1308 OMIM:211750 OMIM:130650 OMIM:616300 OMIM:214800 OMIM:613630 ORPHA:2021 OMIM:228520 ORPHA:63260 ORPHA:254534 ORPHA:254528 ORPHA:96334 OMIM:616894 ORPHA:93271 ORPHA:3366 OMIM:190440 ORPHA:2484 OMIM:309350 ORPHA:90652 OMIM:311300 OMIM:304120 ORPHA:1263 OMIM:265380 ORPHA:2052 OMIM:248450 OMIM:619124 ORPHA:373 ORPHA:531 ORPHA:887 OMIM:236680 OMIM:617895 ORPHA:93930 OMIM:600373 OMIM:222448 ORPHA:2143 OMIM:257920 ORPHA:2273 ORPHA:2745 OMIM:249000 ORPHA:371428 ORPHA:563609 OMIM:617022 OMIM:602535 OMIM:618529 ORPHA:436252 ORPHA:2059 ORPHA:2092 OMIM:305600 OMIM:618820 OMIM:618419 OMIM:610828 OMIM:201000 OMIM:263650 OMIM:145420 ORPHA:1519 OMIM:614450 OMIM:603194 OMIM:618316 OMIM:618454 OMIM:275100 OMIM:243150 ORPHA:920 OMIM:200110 OMIM:306955

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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