MCID: OMP004
MIFTS: 47

Omphalocele

Categories: Fetal diseases, Gastrointestinal diseases, Liver diseases, Rare diseases

Aliases & Classifications for Omphalocele

MalaCards integrated aliases for Omphalocele:

Name: Omphalocele 12 58 54 15
Omphalocoele 12 6
Congenital Omphalocele 70

Characteristics:

Orphanet epidemiological data:

58
omphalocele
Inheritance: Not applicable; Prevalence: 1-5/10000 (Europe),1-5/10000 (Austria),1-5/10000 (Belgium),1-5/10000 (Croatia),1-5/10000 (Denmark),1-5/10000 (France),1-5/10000 (Germany),1-9/100000 (Hungary),1-5/10000 (Ireland),1-5/10000 (Italy),1-5/10000 (Malta),1-5/10000 (Netherlands),1-5/10000 (Norway),1-5/10000 (Poland),1-9/100000 (Spain),1-5/10000 (Switzerland),1-5/10000 (United Kingdom),1-5/10000 (Ukraine),1-5/10000 (United States); Age of onset: Antenatal,Neonatal; Age of death: any age;

Classifications:

Orphanet: 58  
Developmental anomalies during embryogenesis


External Ids:

Disease Ontology 12 DOID:0060327
ICD9CM 34 756.72
MeSH 44 D006554
NCIt 50 C98997
SNOMED-CT 67 49324006 5867007
ICD10 32 Q79.2
ICD10 via Orphanet 33 Q79.2
UMLS via Orphanet 71 C0795690
Orphanet 58 ORPHA660
UMLS 70 C0795690 C1306503

Summaries for Omphalocele

Disease Ontology : 12 A physical disorder characterized by a defect in the development of the abdominal wall muscles, resulting in the intestines, liver and other organs to remain outside of the abdomen in a sac.

MalaCards based summary : Omphalocele, also known as omphalocoele, is related to beckwith-wiedemann syndrome and anus, imperforate. An important gene associated with Omphalocele is PLOD1 (Procollagen-Lysine,2-Oxoglutarate 5-Dioxygenase 1), and among its related pathways/superpathways are Embryonic and Induced Pluripotent Stem Cell Differentiation Pathways and Lineage-specific Markers and Endochondral Ossification. Affiliated tissues include liver, heart and kidney, and related phenotypes are premature birth and omphalocele

Wikipedia : 73 Omphalocele or omphalocoele also called exomphalos, is a rare abdominal wall defect. Beginning at the... more...

Related Diseases for Omphalocele

Diseases in the Omphalocele family:

Omphalocele, Autosomal

Diseases related to Omphalocele via text searches within MalaCards or GeneCards Suite gene sharing:

(show top 50) (show all 281)
# Related Disease Score Top Affiliating Genes
1 beckwith-wiedemann syndrome 31.4 NSD1 KCNQ1OT1 CDKN1C AFP
2 anus, imperforate 30.8 ZIC3 MNX1 GLI3
3 macroglossia 30.5 NSD1 CDKN1C
4 umbilical hernia 30.2 PLOD1 KCNQ1OT1 GLI3 CDKN1C
5 hemihyperplasia, isolated 30.0 KCNQ1OT1 CDKN1C
6 patent ductus arteriosus 1 30.0 ZIC3 NSD1 FLNA
7 apert syndrome 29.9 MSX2 GLI3 ALX4
8 chromosome 2q35 duplication syndrome 29.7 MSX2 MSX1 GLI3 FREM1 ALX4
9 craniosynostosis 29.5 MSX2 MSX1 GLI3 FREM1 ALX4
10 cleft palate, isolated 29.4 NSD1 MSX2 MSX1 GLI3 FLNA BMPR1A
11 dysostosis 29.1 MSX2 GLI3 ALX4
12 meningocele 29.1 MNX1 AFP
13 neural tube defects 29.1 ZIC3 TCN2 MSX2 MSX1 MNX1 GLI3
14 holoprosencephaly 28.9 ZIC3 PPP2R3C MSX2 MSX1 MNX1 GLI3
15 shprintzen omphalocele syndrome 11.6
16 abdominal wall defect 11.6
17 omphalocele-cleft palate syndrome, lethal 11.6
18 omphalocele, autosomal 11.6
19 cloacal exstrophy 11.5
20 oeis complex 11.4
21 gastroschisis 11.3
22 omphalocele, diaphragmatic hernia, and radial ray defects 11.2
23 hydrocephalus with associated malformations 11.2
24 pagod syndrome 11.2
25 manitoba oculotrichoanal syndrome 11.1
26 otopalatodigital syndrome, type ii 11.0
27 boomerang dysplasia 11.0
28 donnai-barrow syndrome 11.0
29 bladder exstrophy and epispadias complex 11.0
30 gonadal dysgenesis, dysmorphic facies, retinal dystrophy, and myopathy 11.0
31 diaphragmatic agenesis radial aplasia omphalocele 10.9
32 omphalocele, x-linked 10.9
33 familial omphalocele syndrome with facial dysmorphism 10.9
34 focal dermal hypoplasia 10.9
35 miller-dieker lissencephaly syndrome 10.9
36 acrocephalopolydactylous dysplasia 10.8
37 fibrochondrogenesis 10.8
38 schisis association 10.8
39 hypertelorism, teebi type 10.8
40 3mc syndrome 3 10.8
41 3mc syndrome 1 10.8
42 3mc syndrome 2 10.8
43 robinow syndrome, autosomal recessive 2 10.8
44 genitourinary and/or brain malformation syndrome 10.8
45 developmental and epileptic encephalopathy 89 10.8
46 froster-huch syndrome 10.8
47 ichthyosis follicularis atrichia photophobia syndrome 10.8
48 methimazole antenatal exposure 10.8
49 chromosomal triplication 10.5
50 pulmonary hypertension 10.3

Graphical network of the top 20 diseases related to Omphalocele:



Diseases related to Omphalocele

Symptoms & Phenotypes for Omphalocele

Human phenotypes related to Omphalocele:

58 31
# Description HPO Frequency Orphanet Frequency HPO Source Accession
1 premature birth 58 31 hallmark (90%) Very frequent (99-80%) HP:0001622
2 omphalocele 58 31 hallmark (90%) Very frequent (99-80%) HP:0001539

MGI Mouse Phenotypes related to Omphalocele:

46 (show all 14)
# Description MGI Source Accession Score Top Affiliating Genes
1 mortality/aging MP:0010768 10.34 AFP ALX4 BMPR1A FLNA FREM1 GLI3
2 growth/size/body region MP:0005378 10.31 ALX4 BMPR1A FLNA FREM1 GLI3 HOXB2
3 craniofacial MP:0005382 10.28 ALX4 BMPR1A FLNA FREM1 GLI3 HOXB2
4 digestive/alimentary MP:0005381 10.22 ALX4 BMPR1A FLNA FREM1 GLI3 MNX1
5 embryo MP:0005380 10.21 ALX4 BMPR1A GLI3 HOXB2 MSX1 MSX2
6 nervous system MP:0003631 10.18 ALX4 BMPR1A FLNA FREM1 GLI3 HOXB2
7 muscle MP:0005369 10.1 ALX4 BMPR1A FREM1 HOXB2 HOXB4 MNX1
8 normal MP:0002873 10.06 ALX4 BMPR1A FLNA FREM1 GLI3 HOXB2
9 limbs/digits/tail MP:0005371 10 ALX4 BMPR1A FREM1 GLI3 MSX1 MSX2
10 hearing/vestibular/ear MP:0005377 9.95 BMPR1A GLI3 HOXB2 MSX1 MSX2 ZIC3
11 respiratory system MP:0005388 9.85 ALX4 BMPR1A FLNA FREM1 GLI3 HOXB2
12 skeleton MP:0005390 9.73 ALX4 BMPR1A FLNA FREM1 GLI3 HOXB2
13 pigmentation MP:0001186 9.65 BMPR1A GLI3 MSX2 NUAK1 NUAK2
14 vision/eye MP:0005391 9.36 ALX4 BMPR1A FLNA FREM1 GLI3 HOXB2

Drugs & Therapeutics for Omphalocele

Interventional clinical trials:


# Name Status NCT ID Phase Drugs
1 Omphaloceles and Associated Malformations in Preterm and Term Newborns Recruiting NCT04126863
2 Neurodevelopmental Outcomes and Growth in Infants With Congenital Gastrointestinal Anomalies Requiring Neonatal Surgery Recruiting NCT04575649

Search NIH Clinical Center for Omphalocele

Genetic Tests for Omphalocele

Anatomical Context for Omphalocele

MalaCards organs/tissues related to Omphalocele:

40
Liver, Heart, Kidney, Skin, Placenta, Spleen, Brain

Publications for Omphalocele

Articles related to Omphalocele:

(show top 50) (show all 2036)
# Title Authors PMID Year
1
CDKN1C (p57(Kip2)) analysis in Beckwith-Wiedemann syndrome (BWS) patients: Genotype-phenotype correlations, novel mutations, and polymorphisms. 54 61
20503313 2010
2
Familial Beckwith-Wiedemann syndrome due to CDKN1C mutation manifesting with recurring omphalocele. 54 61
18395877 2008
3
Syndromes and disorders associated with omphalocele (I): Beckwith-Wiedemann syndrome. 54 61
17638616 2007
4
Mouse mutant embryos overexpressing IGF-II exhibit phenotypic features of the Beckwith-Wiedemann and Simpson-Golabi-Behmel syndromes. 54 61
9389646 1997
5
Second-trimester maternal serum alpha-fetoprotein, unconjugated estriol, and hCG levels in pregnancies with ventral wall defects. 54 61
7524003 1994
6
Amniotic fluid acetylcholinesterase is found in gastroschisis but not omphalocele. 61 54
8240688 1993
7
High levels of maternal serum alpha-fetoprotein and human chorionic gonadotrophins leading to the diagnosis of combined neural tube defect and partial mole. 61 54
1377390 1992
8
Fetal abdominal wall defects in an Australian tertiary setting: contemporary characteristics, ultrasound accuracy, and outcome. 61
31242785 2021
9
Omphalocele in Finland from 1993 to 2014: Trends, Prevalence, Mortality, and Associated Malformations-A Population-Based Study. 61
32131131 2021
10
Prepare for the Rare: Innovation Simulation for Managing Abdominal Wall Defects. 61
33731376 2021
11
Long-term hospital admissions and surgical treatment of children with congenital abdominal wall defects: a population-based study. 61
33666724 2021
12
Turbulent Cerebrospinal Fluid Flow in Enlarging Terminal Myelocystocele. 61
33348100 2021
13
Perioperative anesthetic management of reductive glossoplasty in a patient with Beckwith-Wiedemann syndrome. 61
32417109 2021
14
Omphalocele-What should we tell the prospective parents? 61
33540475 2021
15
Rapidly involuting congenital hemangioma of the liver in a newborn with incomplete Pentalogy of Cantrell: description of a new association. 61
33777350 2021
16
Monochorionic Triplet Pregnancies With Twin Reversed Arterial Perfusion and Acardiac Triplet: Report of Two Cases and Literature Review. 61
33439111 2021
17
Complex abdominal wall reconstruction after oncologic resection in a sequalae of giant omphalocele: A case report. 61
33691272 2021
18
Twin pregnancy in which both fetuses have Cantrell's pentalogy: A case report and literature review. 61
33743359 2021
19
Prenatal diagnosis of intestinal nonrotation using magnetic resonance imaging: Is it possible? 61
33608743 2021
20
Incisional hernia after abdominal surgery in infants: A retrospective analysis of incidence and risk factors. 61
33618851 2021
21
Abdominal Wall Defects-Current Treatments. 61
33672248 2021
22
Surgical management of omphalocele with double outlet of right ventricle and biliary atresia: A case report. 61
33248895 2021
23
Omphalomesenteric duct in a neonate with omphalocele minor. 61
33627330 2021
24
Can cell-free DNA testing be used in pregnancies with isolated fetal omphalocele? Preliminary evidence from cytogenetic results of prenatal cases. 61
31018788 2021
25
Giant Omphalocele Complicated by 9P Minus Syndrome. 61
32747314 2021
26
Prenatal diagnosis of tibial hemimelia type I and omphalocele, a rare entity and postnatal correlation. 61
33614110 2021
27
Successful closure of a large abdominal wall defect using endoscopic component separation technique in an infant with a giant ventral hernia after staged surgery for omphalocele. 61
33409717 2021
28
Investigation of a connection between abdominal wall defects and severity of the herniation in fetuses with gastroschisis and omphalocele. 61
33420099 2021
29
Congenital abdominal wall defects and cryptorchidism: a population-based study. 61
33517489 2021
30
Safety of delayed surgical repair of omphalocele-exstrophy-imperforate anus-spinal defects (OEIS) complex in infants with significant comorbidities. 61
33231719 2021
31
Education of pediatric surgery residents over time: Examining 15 years of case logs. 61
33139026 2021
32
Folic acid supplementation and risk for fetal abdominal wall defects in China: results from a large population-based intervention cohort study. 61
33494841 2021
33
Mortality in neonates with giant omphalocele subjected to a surgical technique in Barranquilla, Colombia from 1994 to 2019. 61
33431922 2021
34
Giant omphalocele: Delayed closure using the San Martin technique following epithelialization of the membrane. 61
33487462 2021
35
Histomorphology of the lesions of the umbilicus: Are we naïve about the navel? 61
33433415 2021
36
Fetal glycosylation defect due to ALG3 and COG5 variants detected via amniocentesis: Complex glycosylation defect with embryonic lethal phenotype. 61
33187827 2020
37
Congenital diaphragmatic hernia as a prominent feature of a SPECC1L-related syndrome. 61
32954677 2020
38
Antibiotic Utilization and Infection Among Infants with Abdominal Wall Defects. 61
32826725 2020
39
Modified sequential sac ligation and staged closure technique for the management of giant omphalocele. 61
33386134 2020
40
A multi-country study of prevalence and early childhood mortality among children with omphalocele. 61
33067932 2020
41
Management of giant omphalocele with a simple and efficient nonsurgical silo. 61
33341259 2020
42
Ventral hernia secondary to giant omphalocele in a child: combined approach of botulinum toxin and preoperative progressive pneumoperitoneum. 61
31858310 2020
43
Quantification of selection bias in studies of risk factors for birth defects among livebirths. 61
32249969 2020
44
Prevalence rates study of selected isolated non-Mendelian congenital anomalies in the Hutterite population of Alberta, 1980-2016. 61
32893972 2020
45
Birth defects that co-occur with non-syndromic gastroschisis and omphalocele. 61
32885608 2020
46
Extended spectrum penicillins reduce the risk of omphalocele: A population-based case-control study. 61
33250216 2020
47
Use of Cryopreserved Human Umbilical Cord and Amniotic Membrane Allograft and Portable Negative Pressure Therapy in Dehisced Giant Omphalocele Repair: A Case Study. 61
33201150 2020
48
Comparison of outcomes of infants with giant omphaloceles over two decades. 61
33164950 2020
49
[Alveolar capillary dysplasia with misalignment of the pulmonary veins: a case report and literature review]. 61
32987465 2020
50
Congenital diaphragmatic hernia and associated omphalocele: a study from the CDHSG registry. 61
31870561 2020

Variations for Omphalocele

ClinVar genetic disease variations for Omphalocele:

6
# Gene Name Type Significance ClinVarId dbSNP ID Position
1 PLOD1 NM_000302.4(PLOD1):c.1562G>A (p.Trp521Ter) SNV Pathogenic 374077 rs1057518879 GRCh37: 1:12025628-12025628
GRCh38: 1:11965571-11965571
2 PGAP2 NM_014489.4(PGAP2):c.97G>A (p.Ala33Thr) SNV Uncertain significance 816936 rs1564998996 GRCh37: 11:3832586-3832586
GRCh38: 11:3811356-3811356
3 LAMA5 NM_005560.6(LAMA5):c.857G>T (p.Arg286Leu) SNV Uncertain significance 986382 GRCh37: 20:60926966-60926966
GRCh38: 20:62351910-62351910

Copy number variations for Omphalocele from CNVD:

7
# CNVD ID Chromosome Start End Type Gene Symbol CNVD Disease
1 137137 2 138750000 144750000 Deletion ARHGAP15 Omphalocele
2 137141 2 138750000 144750000 Deletion GTDC1 Omphalocele
3 137145 2 138750000 144750000 Deletion HNMT Omphalocele
4 137149 2 138750000 144750000 Deletion KYNU Omphalocele
5 137153 2 138750000 144750000 Deletion Omphalocele
6 137157 2 138750000 144750000 Deletion LRP1B Omphalocele
7 137161 2 138750000 144750000 Deletion NXPH2 Omphalocele
8 137165 2 138750000 144750000 Deletion SPOPL Omphalocele

Expression for Omphalocele

Search GEO for disease gene expression data for Omphalocele.

Pathways for Omphalocele

Pathways related to Omphalocele according to GeneCards Suite gene sharing:

# Super pathways Score Top Affiliating Genes
1 11.26 MSX1 BMPR1A AFP
2 10.61 GLI3 CDKN1C BMPR1A

GO Terms for Omphalocele

Cellular components related to Omphalocele according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 chromatin GO:0000785 9.5 NSD1 MSX2 MSX1 MNX1 HOXB4 HOXB2
2 nucleus GO:0005634 9.47 ZIC3 PPP2R3C NUAK2 NUAK1 NSD1 MSX2

Biological processes related to Omphalocele according to GeneCards Suite gene sharing:

(show all 20)
# Name GO ID Score Top Affiliating Genes
1 regulation of transcription by RNA polymerase II GO:0006357 10.15 ZIC3 MSX2 MSX1 MNX1 HOXB4 HOXB2
2 multicellular organism development GO:0007275 10.08 ZIC3 MSX2 MSX1 HOXB4 HOXB2 FREM1
3 positive regulation of transcription by RNA polymerase II GO:0045944 10.07 ZIC3 MSX1 HOXB4 HOXB2 GLI3 BMPR1A
4 regulation of transcription, DNA-templated GO:0006355 10.06 NSD1 MSX2 MSX1 MNX1 HOXB4 HOXB2
5 lung development GO:0030324 9.76 ZIC3 GLI3 BMPR1A
6 odontogenesis of dentin-containing tooth GO:0042475 9.69 MSX1 GLI3 BMPR1A
7 roof of mouth development GO:0060021 9.67 MSX1 GLI3 BMPR1A ALX4
8 heart morphogenesis GO:0003007 9.65 MSX1 FLNA BMPR1A
9 pattern specification process GO:0007389 9.62 ZIC3 GLI3 BMPR1A ALX4
10 skeletal system morphogenesis GO:0048705 9.61 HOXB4 HOXB2 ALX4
11 limb morphogenesis GO:0035108 9.59 GLI3 ALX4
12 regulation of cellular senescence GO:2000772 9.58 NUAK1 BMPR1A
13 dorsal/ventral pattern formation GO:0009953 9.58 HOXB2 GLI3 BMPR1A
14 negative regulation of transcription regulatory region DNA binding GO:2000678 9.57 MSX2 MSX1
15 morphogenesis of an epithelial sheet GO:0002011 9.56 HOXB4 HOXB2
16 embryonic digit morphogenesis GO:0042733 9.56 MSX1 GLI3 BMPR1A ALX4
17 BMP signaling pathway involved in heart development GO:0061312 9.49 MSX1 BMPR1A
18 embryonic skeletal system morphogenesis GO:0048704 9.46 HOXB4 HOXB2 GLI3 ALX4
19 embryonic morphogenesis GO:0048598 9.26 MSX2 MSX1 GLI3 BMPR1A
20 anterior/posterior pattern specification GO:0009952 9.17 ZIC3 MSX1 HOXB4 HOXB2 GLI3 BMPR1A

Molecular functions related to Omphalocele according to GeneCards Suite gene sharing:

# Name GO ID Score Top Affiliating Genes
1 metal ion binding GO:0046872 10.06 ZIC3 TCN2 PPP2R3C PLOD1 NUAK2 NUAK1
2 DNA binding GO:0003677 10.01 ZIC3 MSX2 MSX1 MNX1 HOXB4 HOXB2
3 DNA-binding transcription factor activity GO:0003700 9.77 ZIC3 HOXB4 HOXB2 GLI3 ALX4
4 DNA-binding transcription factor activity, RNA polymerase II-specific GO:0000981 9.76 ZIC3 MSX2 MSX1 MNX1 HOXB4 HOXB2
5 RNA polymerase II regulatory region sequence-specific DNA binding GO:0000977 9.65 ZIC3 MSX2 MSX1 GLI3 ALX4
6 sequence-specific DNA binding GO:0043565 9.43 ZIC3 MSX2 MSX1 HOXB2 GLI3 ALX4
7 sequence-specific double-stranded DNA binding GO:1990837 9.23 ZIC3 MSX2 MSX1 MNX1 HOXB4 HOXB2

Sources for Omphalocele

3 CDC
7 CNVD
9 Cosmic
10 dbSNP
11 DGIdb
17 EFO
18 ExPASy
19 FMA
20 GARD
28 GO
29 GTR
30 HMDB
31 HPO
32 ICD10
33 ICD10 via Orphanet
34 ICD9CM
35 IUPHAR
36 KEGG
37 LifeMap
39 LOVD
41 MedGen
44 MeSH
45 MESH via Orphanet
46 MGI
49 NCI
50 NCIt
51 NDF-RT
53 NINDS
54 Novoseek
56 OMIM via Orphanet
57 OMIM® (Updated 20-May-2021)
61 PubMed
63 QIAGEN
68 SNOMED-CT via HPO
69 Tocris
70 UMLS
71 UMLS via Orphanet
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