🏷

Classifications

Harrison's Part

🔗

Mappings

MONDO

MONDO:0019015 omphalocele

MONDO:0019015 (omphalocele) is the disease term for this entry; it lists Orphanet:660, NCIT:C98997, and ICD-10 Q79.2 cross-references.

👪

Inheritance

1

Chromosomal and Syndromic HP:0001426

Non-isolated and syndromic omphalocele follows the chromosomal or syndromic inheritance pattern of the underlying condition; chromosomal abnormalities (such as trisomy 18 and trisomy 13) and congenital syndromes account for a large fraction of cases.

Non-Mendelian inheritance

Show evidence (1 reference)

PMID:34392395 SUPPORT Human clinical

"About 62% of the cases had associated malformations and/or genetic disorders; most common was ventricular septal defect."

Supports the high proportion of omphalocele cases associated with genetic and chromosomal disorders.

◆

Subtypes

3

Isolated (non-syndromic) omphalocele

Omphalocele occurring without associated major malformations, chromosomal abnormality, or recognized syndrome. Isolated cases have the most favorable prognosis, with high survival in the absence of chromosomal defects.

Show evidence (1 reference)

PMID:32131131 SUPPORT Human clinical

"Total 1-year survival rates for isolated omphalocele, cases with multiple anomalies and neonates with chromosomal defects were 80, 88, and 17%, respectively."

Distinguishes isolated omphalocele from cases with multiple anomalies or chromosomal defects and quantifies its higher 1-year survival rate.

Syndromic / chromosomal omphalocele

Omphalocele occurring as part of a recognized congenital syndrome or chromosomal abnormality (such as trisomy 18, trisomy 13, or Beckwith-Wiedemann syndrome). Carries substantially worse prognosis, driven by the associated anomalies and chromosomal or syndromic diagnosis.

Show evidence (2 references)

PMID:39576336 SUPPORT Human clinical

"Over one-half (53.7%) presented with one or more major malformations, and an additional 17.0% were diagnosed with a syndrome."

Documents the syndromic and malformation-associated subgroup in a nationwide birth cohort.

PMID:40150018 SUPPORT Human clinical

"While omphalocele can occur as an isolated anomaly, it is more commonly associated with congenital syndromes and structural abnormalities."

Confirms that omphalocele is commonly associated with congenital syndromes and structural abnormalities.

Giant omphalocele

Anatomic size and severity stratum (which can occur in either isolated or syndromic omphalocele) characterized by viscero-abdominal disproportion that prevents primary fascial closure and predisposes to pulmonary hypoplasia and pulmonary hypertension.

Show evidence (1 reference)

PMID:40389219 SUPPORT Human clinical

"Giant omphalocele is appropriately defined as viscero-abdominal disproportion preventing primary closure."

Provides the European Paediatric Surgeons' Association consensus definition of giant omphalocele.

⚙

Pathophysiology

4

Ventral Body Wall Closure Failure

The primary developmental lesion in omphalocele is failure to complete normal ventral body wall formation at the umbilical region. During normal embryogenesis the lateral, cephalic, and caudal body folds migrate ventrally and fuse at the umbilical ring; failure of this morphogenetic process leaves a central defect through which abdominal viscera herniate into the base of the umbilical cord, covered by a membranous (peritoneum/Wharton's jelly/amnion) sac. This distinguishes omphalocele from gastroschisis (a paraumbilical defect without a sac).

Body wall mesenchymal cell CL:0000134 Body wall fibroblast CL:0000057

Embryonic body morphogenesis (ventral body wall closure) GO:0010172 ⚠ ABNORMAL Mesenchymal cell migration (body-fold migration) GO:0090497 ↓ DECREASED Umbilical cord morphogenesis GO:0036304 ⚠ ABNORMAL

abdominal wall UBERON:0003697 umbilical cord UBERON:0002331

Downstream

Midgut Herniation and Viscero-Abdominal Disproportion Failure of ventral body wall closure leaves an open umbilical-ring defect through which abdominal viscera herniate into the membrane-covered sac.

Omphalocele (ventral abdominal wall defect) Incomplete ventral abdominal wall closure directly manifests as the congenital omphalocele defect at the base of the umbilical cord.

Show evidence (2 references)

PMID:38021990 SUPPORT Human clinical

"Omphalocele refers to the herniation of abdominal contents through a defect in the abdominal wall at the umbilicus with or without the presence of a sac."

Review defining omphalocele as herniation of abdominal contents through a ventral abdominal wall defect at the umbilicus, the anatomic consequence of failed ventral body wall closure.

PMID:37726736 SUPPORT Human clinical

"Patients with omphalocele, a midline abdominal wall defect at the umbilical cord base, have a low survival rate."

Confirms the midline umbilical-base location of the abdominal wall defect that defines omphalocele.

Midgut Herniation and Viscero-Abdominal Disproportion

Abdominal viscera - intestine and, in large/giant defects, the liver - herniate through the body wall defect into the sac. In normal development a physiologic midgut herniation occurs at ~6-10 weeks' gestation and returns to the abdominal cavity; persistence/failure of this return contributes to the pathologic herniation. The resulting reduction in intra-abdominal domain produces viscero-abdominal disproportion, which both complicates surgical reduction (risk of abdominal compartment syndrome) and, in giant defects, constrains thoraco-abdominal development.

Hepatocyte (herniated liver) CL:0000182

Midgut development GO:0007494 ⚠ ABNORMAL

abdominal wall UBERON:0003697 liver UBERON:0002107

Downstream

Pulmonary Hypoplasia Viscero-abdominal disproportion in large/giant defects reduces the intra-abdominal domain and constrains thoraco-abdominal development, restricting fetal lung expansion.

Show evidence (2 references)

PMID:38021990 SUPPORT Human clinical

"Omphalocele refers to the herniation of abdominal contents through a defect in the abdominal wall at the umbilicus with or without the presence of a sac."

Supports herniation of abdominal contents (midgut, and in large defects liver) through the umbilical defect; the abstract does not separately quantify viscero-abdominal disproportion.

PMID:40150018 SUPPORT Human clinical

"giant omphaloceles are frequently linked to lung hypoplasia, as reduced intra-abdominal space restricts fetal lung expansion"

Supports that reduced intra-abdominal space (viscero-abdominal disproportion) in giant omphalocele restricts fetal development.

Pulmonary Hypoplasia

In large/giant omphalocele the reduced intra-abdominal domain and abnormal thoraco-abdominal dynamics constrain fetal lung expansion, producing pulmonary hypoplasia with structural lung and vascular developmental abnormalities.

Lung development GO:0030324 ↓ DECREASED

lung UBERON:0002048

Downstream

Pulmonary hypoplasia Restricted fetal thoracic and intra-abdominal space directly impairs lung growth, causing clinical pulmonary hypoplasia.

Pulmonary Hypertension Structural lung hypoplasia and impaired pulmonary vascular development in giant omphalocele lead to increased pulmonary vascular resistance and pulmonary hypertension.

Respiratory insufficiency Pulmonary hypoplasia directly impairs neonatal gas exchange and causes severe respiratory insufficiency.

Show evidence (1 reference)

PMID:40150018 SUPPORT Human clinical

"giant omphaloceles are frequently linked to lung hypoplasia, as reduced intra-abdominal space restricts fetal lung expansion, leading to structural lung abnormalities and increased pulmonary vascular resistance."

Supports the mechanistic link from restricted fetal lung expansion to pulmonary hypoplasia and structural lung abnormalities.

Pulmonary Hypertension

Impaired pulmonary vascular development and structural lung hypoplasia in giant omphalocele elevate pulmonary vascular resistance, producing neonatal pulmonary hypertension and hypoxemic respiratory distress.

Pulmonary artery endothelial cell CL:1001568 Pulmonary arterial smooth muscle cell CL:0002591

Pulmonary vasculature development GO:0001944 ⚠ ABNORMAL

lung UBERON:0002048

Downstream

Pulmonary hypertension Impaired pulmonary vascular development and elevated pulmonary vascular resistance manifest clinically as neonatal pulmonary hypertension.

Respiratory insufficiency Elevated pulmonary vascular resistance and pulmonary hypertension cause hypoxemia and severe neonatal respiratory insufficiency.

Show evidence (1 reference)

PMID:40150018 SUPPORT Human clinical

"Among its most significant complications, pulmonary hypoplasia (PH) and pulmonary hypertension (PPH) have been shown to negatively impact neonatal prognosis. These conditions result from impaired pulmonary vascular development, leading to respiratory distress and hypoxemia."

Directly supports pulmonary hypertension arising from impaired pulmonary vascular development in omphalocele.

⬡

Pathograph

Use Group by to collapse related nodes into one box. Use the checkboxes to hide or show graph categories. Hover nodes for evidence and cross-linked metadata.

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Phenotypes

7

Cardiovascular 3

Congenital heart defects FREQUENT Abnormal heart morphology HP:0001627

Show evidence (1 reference)

PMID:37189937 SUPPORT Human clinical

"in patients with omphalocele, cardiac anomalies were most identified (n = 15, 37.5%)"

Supports congenital heart defects as the most common associated anomaly in omphalocele, present in 37.5% of the cohort.

Ventricular septal defect HP:0001629

Show evidence (1 reference)

PMID:34392395 SUPPORT Human clinical

"About 62% of the cases had associated malformations and/or genetic disorders; most common was ventricular septal defect."

Supports ventricular septal defect as the most common associated malformation in a national cohort.

Pulmonary hypertension Pulmonary arterial hypertension HP:0002092

Show evidence (1 reference)

PMID:40150018 SUPPORT Human clinical

"Severe respiratory insufficiency, particularly due to pulmonary hypoplasia and pulmonary hypertension, significantly increases neonatal morbidity and mortality."

Supports pulmonary hypertension as a contributor to neonatal morbidity and mortality.

Digestive 2

Omphalocele (ventral abdominal wall defect) OBLIGATE HP:0001539

Onset: CONGENITAL

Show evidence (1 reference)

PMID:38021990 SUPPORT Human clinical

"Omphalocele refers to the herniation of abdominal contents through a defect in the abdominal wall at the umbilicus with or without the presence of a sac."

Defines the core omphalocele phenotype.

Feeding difficulties HP:0011968

Show evidence (1 reference)

PMID:38376641 SUPPORT Human clinical

"The average time taken to reach full feeds was 1 week; only one patient required parenteral nutrition."

A case series of exomphalos major tracks time to full feeds, reflecting feeding difficulty as a clinically relevant sequela.

Respiratory 2

Pulmonary hypoplasia HP:0002089

Show evidence (1 reference)

PMID:40150018 SUPPORT Human clinical

"Among its most significant complications, pulmonary hypoplasia (PH) and pulmonary hypertension (PPH) have been shown to negatively impact neonatal prognosis."

Supports pulmonary hypoplasia as a significant complication.

Respiratory insufficiency HP:0002093

Show evidence (1 reference)

PMID:40150018 SUPPORT Human clinical

"Severe respiratory insufficiency, particularly due to pulmonary hypoplasia and pulmonary hypertension, significantly increases neonatal morbidity and mortality."

Supports severe respiratory insufficiency as a major morbidity.

🧬

Genetic Associations

3

Chromosomal aneuploidy (trisomy 13, 18, 21)

Chromosomal

Show evidence (1 reference)

PMID:34392395 SUPPORT Human clinical

"About 62% of the cases had associated malformations and/or genetic disorders; most common was ventricular septal defect."

Supports the high proportion of omphalocele cases with associated genetic disorders, including chromosomal abnormalities.

Associated chromosomal abnormalities (population estimate)

Chromosomal

Show evidence (1 reference)

PMID:32131131 SUPPORT Human clinical

"most commonly chromosomal abnormalities (9.3%), heart defects (6.3%), central nervous system anomalies (3.0%)"

Supports chromosomal abnormalities as the most common associated anomaly in a population-based omphalocele cohort.

Monogenic variants in selected non-isolated cases

Show evidence (1 reference)

PMID:37726736 SUPPORT Human clinical

"Six nonisolated cases had normal CMA results and conventional karyotype tests, and further WES examination revealed one pathogenic variant and two suspected pathogenic variants."

Supports a monogenic contribution detectable by WES in selected non-isolated omphalocele cases with normal karyotype/CMA.

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Medical Actions

5

Primary surgical closure

Action: surgical procedure Ontology label: Surgical Procedure NCIT:C15329

Platform: Surgery

Definitive early operative reduction of herniated viscera and closure of the abdominal wall defect. Best suited to small omphaloceles or cases without major viscero-abdominal disproportion; urgent reduction can dangerously raise intra-abdominal pressure and precipitate abdominal compartment syndrome.

Mechanism Target:

RESTORES Ventral Body Wall Closure Failure — Operative fascial repair directly closes the congenital ventral abdominal wall defect in patients without prohibitive viscero-abdominal disproportion.

Show evidence (1 reference)

PMID:40389219 SUPPORT INDIRECT Human clinical

"Giant omphalocele is appropriately defined as viscero-abdominal disproportion preventing primary closure."

Supports primary surgical closure as the standard restorative approach when viscero-abdominal disproportion does not prevent primary closure.

Show evidence (1 reference)

PMID:40389219 SUPPORT Human clinical

"Giant omphalocele is appropriately defined as viscero-abdominal disproportion preventing primary closure."

The EUPSA consensus defines giant omphalocele by viscero-abdominal disproportion that precludes primary closure, indicating primary closure is the approach for non-giant defects.

Staged / traction-assisted closure

Action: surgical procedure Ontology label: Surgical Procedure NCIT:C15329

Platform: Surgery

Staged reduction (e.g., silo) or vertical traction-assisted staged closure is used when primary closure is unsafe because of a large defect, liver herniation, or marked viscero-abdominal disproportion. A prospective device series achieved complete fascial closure in all 16 patients (10 giant omphalocele, 6 gastroschisis) with no abdominal compartment syndrome.

Mechanism Target:

RESTORES Midgut Herniation and Viscero-Abdominal Disproportion — Gradual staged or vertical-traction reduction accommodates herniated viscera and expands the intra-abdominal domain before definitive fascial closure.

Show evidence (1 reference)

PMID:38960901 SUPPORT Human clinical

"Complete fascial closure was achieved after a median time of 7 days (range 4-22) in GOC and 5 days (range 4-11) in GS."

Demonstrates that traction-assisted staged reduction overcomes viscero-abdominal disproportion to achieve complete fascial closure.

Show evidence (1 reference)

PMID:38960901 SUPPORT Human clinical

"Complete fascial closure was achieved after a median time of 7 days (range 4-22) in GOC and 5 days (range 4-11) in GS."

Supports traction-assisted staged closure achieving complete fascial closure in giant omphalocele and gastroschisis.

Conservative "paint and wait" management

Action: topical pharmacotherapy Ontology label: Pharmacotherapy NCIT:C15986

Platform: Small molecule

Non-operative topical epithelialization of the intact sac, recommended when anatomical constraints or high surgical risk preclude primary closure (especially giant omphalocele with liver exteriorization and/or pulmonary hypoplasia/hypertension). Common painting agents include povidone-iodine and silver sulfadiazine. Later definitive ventral hernia repair is often needed.

Mechanism Target:

MODULATES Midgut Herniation and Viscero-Abdominal Disproportion — Topical escharotic therapy epithelializes the intact sac while deferring visceral reduction and fascial closure until later, avoiding acute increases in intra-abdominal pressure when viscero-abdominal disproportion precludes primary surgical closure.

Show evidence (1 reference)

PMID:40389219 SUPPORT Human clinical

"the "paint and wait" approach is recommended when anatomical constraints or high surgical risk preclude primary closure. Common painting agents include povidone-iodine and silver sulfadiazine"

Supports topical escharotic sac management when anatomical constraints (viscero-abdominal disproportion) or surgical risk preclude primary closure.

Show evidence (1 reference)

PMID:40389219 SUPPORT Human clinical

"the "paint and wait" approach is recommended when anatomical constraints or high surgical risk preclude primary closure. Common painting agents include povidone-iodine and silver sulfadiazine"

EUPSA consensus recommends paint-and-wait conservative topical management when primary closure is precluded.

Awake graduated compression dressing

Action: supportive care Ontology label: Supportive Care NCIT:C15747

Platform: Other

A bedside, awake gradual compression dressing technique for exomphalos major that reduces sac contents without general anaesthetic or respiratory compromise and permits simultaneous early enteral feeding.

Mechanism Target:

RESTORES Midgut Herniation and Viscero-Abdominal Disproportion — Gradual external compression reduces herniated sac contents without precipitating respiratory compromise.

Show evidence (1 reference)

PMID:38376641 SUPPORT Human clinical

"This case series describes a successful compression dressing technique that reduces sac content without the need for general anaesthetic or respiratory compromise, whereby simultaneous enteral feeding is tolerated."

Demonstrates that awake graduated compression dressing reduces herniated sac contents without respiratory compromise.

Show evidence (1 reference)

PMID:38376641 SUPPORT Human clinical

"This case series describes a successful compression dressing technique that reduces sac content without the need for general anaesthetic or respiratory compromise, whereby simultaneous enteral feeding is tolerated."

Supports awake graduated compression dressing as a conservative bedside reduction strategy for exomphalos major.

Genetic counseling

Action: Genetic Counseling NCIT:C15240

Platform: Other

Genetic counseling addresses the high rate of associated chromosomal abnormalities and congenital syndromes in omphalocele and their prognostic and recurrence implications.

Show evidence (1 reference)

PMID:39576336 SUPPORT Human clinical

"Over one-half (53.7%) presented with one or more major malformations, and an additional 17.0% were diagnosed with a syndrome."

The high burden of co-occurring malformations and syndromes supports the role of genetic counseling.

🔬

Diagnosis

3

Prenatal ultrasonography

Prenatal ultrasound identifies the midline ventral abdominal wall defect at the base of the umbilical cord, characterizes herniated contents (such as liver), and screens for co-occurring structural malformations to classify isolated versus non-isolated omphalocele.

Fetal Ultrasound Imaging NCIT:C222238

Results: Demonstration of a membrane-covered midline umbilical-base abdominal wall defect and assessment for associated anomalies.

Show evidence (1 reference)

PMID:37726736 SUPPORT Human clinical

"Among the 120 fetuses, 27 were diagnosed with isolated omphalocele and 93 with nonisolated omphalocele using prenatal ultrasonography."

Establishes prenatal ultrasonography as the primary modality for detecting associated malformations and classifying omphalocele.

Karyotyping and chromosomal microarray analysis

Conventional karyotyping combined with chromosomal microarray analysis (CMA) is recommended for all fetuses diagnosed with omphalocele to identify aneuploidies and pathogenic copy-number variants.

Microarray Analysis NCIT:C18477

Results: Detection of chromosomal aneuploidy or submicroscopic copy-number variants in syndromic/chromosomal omphalocele.

Show evidence (1 reference)

PMID:37726736 SUPPORT Human clinical

"Routine karyotyping with CMA testing should be provided for fetuses with omphalocele. WES is an option if karyotype and CMA tests are normal."

Supports routine prenatal karyotyping and chromosomal microarray testing for fetuses with omphalocele.

Whole exome sequencing

Whole exome sequencing (WES) is used as a reflex diagnostic test in non-isolated omphalocele when conventional karyotyping and chromosomal microarray analysis are normal.

Whole Exome Sequencing NCIT:C101295

Results: Identification of pathogenic or likely pathogenic single-gene variants in non-isolated omphalocele.

Show evidence (1 reference)

PMID:37726736 SUPPORT Human clinical

"Six nonisolated cases had normal CMA results and conventional karyotype tests, and further WES examination revealed one pathogenic variant and two suspected pathogenic variants."

Demonstrates diagnostic yield of WES in non-isolated omphalocele with normal karyotype and CMA.

📈

Progression

1

Neonatal outcome (chromosome/anomaly dependent)

Omphalocele is congenital and frequently diagnosed prenatally by ultrasound. Prognosis is driven primarily by associated anomalies and chromosomal/ syndromic diagnoses rather than the abdominal wall defect alone; in the absence of chromosomal defects survival is reasonably good. In the Finnish cohort, 1-year survival was 80% for isolated omphalocele versus 17% for neonates with chromosomal defects.

Show evidence (2 references)

PMID:32131131 SUPPORT Human clinical

"Total 1-year survival rates for isolated omphalocele, cases with multiple anomalies and neonates with chromosomal defects were 80, 88, and 17%, respectively."

Quantifies the large survival difference between isolated and chromosomally abnormal omphalocele.

PMID:32131131 SUPPORT Human clinical

"In the absence of chromosomal defects, survival is reasonably good."

Supports good survival when chromosomal defects are absent.

📊

Prevalence

2

Danish live births (1997-2021)

Prevalence at birth 9.8 per 100,000 1–9 per 100,000 (births)

Danish nationwide live-birth register study: omphalocele birth prevalence of 0.98 per 10,000 infants (95% CI 0.83-1.15). Over half (53.7%) had one or more major malformations and an additional 17.0% had a diagnosed syndrome.

Show evidence (1 reference)

PMID:39576336 SUPPORT Human clinical

"Among 1,498,685 live births, 147 infants with omphalocele were identified, yielding a combined and stable prevalence (per 10,000 infants) of 0.98 (95% CI 0.83-1.15). Over one-half (53.7%) presented with one or more major malformations, and an additional 17.0% were diagnosed with a syndrome."

Provides nationwide live-birth prevalence and the proportion of cases with co-occurring major malformations and syndromes.

Finnish births (1993-2014, including terminations)

Prevalence at birth 19.6 per 100,000 1–9 per 10,000 (births)

Finnish population-based register study including terminations: total prevalence 4.71 per 10,000 births, birth prevalence 1.96 per 10,000, with 55% of pregnancies terminated.

Show evidence (1 reference)

PMID:32131131 SUPPORT Human clinical

"Birth prevalence in Finland was 1.96 per 10,000 births with no consistent trend over time. However, total prevalence was much higher (4.71/10,000) because more than half of these families chose option for the termination of pregnancy."

Provides total and birth prevalence including terminations, and the high termination rate.

🔀

Differential Diagnoses

1

Conditions with similar clinical presentations that must be differentiated from Omphalocele:

Gastroschisis

Overlapping Features Congenital paraumbilical abdominal wall defect with evisceration of bowel lacking a covering membranous sac and displaying a distinct pattern of associated anomalies (predominantly intestinal rather than cardiac or chromosomal).

Distinguishing Features

Paraumbilical defect without a covering peritoneal/amniotic sac, whereas omphalocele occurs at the umbilical cord base with a sac.
Associated anomalies in gastroschisis are predominantly intestinal, whereas cardiac and chromosomal anomalies predominate in omphalocele.

Show evidence (1 reference)

PMID:37189937 SUPPORT Human clinical

"In patients with gastroschisis, intestinal anomalies were most identified (n = 13, 15.9%), whereas, in patients with omphalocele, cardiac anomalies were most identified (n = 15, 37.5%)."

Contrasts the anomaly profiles of gastroschisis and omphalocele in a comparative cohort study.

📊

Related Datasets

3

Hand1 gene replacement with Hand2 reveals overlap in function with unique occurrence of omphalocele and heart defects [scRNA-seq] geo:GSE299253

The bHLH transcription factors HAND1 and HAND2 are expressed in partially overlapping patterns during development. Studies have established evidence for significant functional redundancy between HAND1 and HAND2. To test redundancy fully, we engineered a Hand1 allele where we directly replace the exons and intron with those of Hand2. Results show that 2% of Hand1Hand2/ Hand2 mice are viable, and fertile. The remaining Hand1Hand2/Hand2 embryos exhibit neonatal lethality due to omphalocele, ventricular septal defects and conduction anomalies.

mouse SINGLE CELL RNA SEQ n=9

PMID:40960281

Identified by GEO DataSets index search for Omphalocele (scripts/discover_datasets.py); accession and metadata verified against NCBI E-utilities on 2026-08-01. Title, sample count, and organism are GEO's own values.

Hand1 gene replacement with Hand2 reveals overlap in function with unique occurrence of omphalocele and heart defects geo:GSE299579

mouse BULK RNA SEQ n=24

Identified by GEO DataSets index search for Omphalocele (scripts/discover_datasets.py); accession and metadata verified against NCBI E-utilities on 2026-08-01. Title, sample count, and organism are GEO's own values.

Hand1 gene replacement with Hand2 reveals overlap in function with unique occurrence of omphalocele and heart defects [Spatial Transcriptomics] geo:GSE298742

The bHLH transcription factors HAND1 and HAND2 are expressed in partially overlapping patterns during development. Studies have established evidence for significant functional redundancy between HAND1 and HAND2. To test redundancy fully, we engineered a Hand1 allele where we directly replace the exons and intron with those of Hand2. Results show that 2% of Hand1Hand2/ Hand2 mice are viable, and fertile. The remaining Hand1Hand2/Hand2 embryos exhibit neonatal lethality due to omphalocele, ventricular septal defects and conduction anomalies.

mouse SPATIAL TRANSCRIPTOMICS n=15

Identified by GEO DataSets index search for Omphalocele (scripts/discover_datasets.py); accession and metadata verified against NCBI E-utilities on 2026-08-01. Title, sample count, and organism are GEO's own values.

{ }

Source YAML

click to show

name: Omphalocele
creation_date: "2026-06-15T00:00:00Z"
description: >-
  Omphalocele (exomphalos) is a congenital midline ventral abdominal wall defect
  at the base of the umbilical cord in which abdominal viscera herniate outside
  the abdomen, typically protected by a membranous sac composed of peritoneum,
  Wharton's jelly, and amnion. It arises from a developmental defect of ventral
  body wall formation, with persistence of the normal physiologic midgut
  herniation (which occurs at roughly 6-10 weeks' gestation and normally returns
  to the abdomen). Defects are commonly classified as small (no liver herniation)
  versus large/giant (liver herniation with viscero-abdominal disproportion).
  Omphalocele is etiologically heterogeneous: many cases are sporadic, but a
  substantial subset is associated with aneuploidy (trisomy 13, 18, 21),
  chromosomal rearrangements, and genetic syndromes (notably
  Beckwith-Wiedemann syndrome). Associated malformations - especially congenital
  heart defects - and chromosomal/syndromic diagnoses are the principal
  determinants of prognosis, rather than the abdominal wall defect alone.
category: Congenital
disease_term:
  preferred_term: Omphalocele
  term:
    id: MONDO:0019015
    label: omphalocele
synonyms:
- Exomphalos
- Congenital omphalocele
- Exomphalos major
- Giant omphalocele
parents:
- Abdominal wall malformation
mappings:
  mondo_mappings:
  - term:
      id: MONDO:0019015
      label: omphalocele
    mapping_predicate: skos:exactMatch
    mapping_source: MONDO
    mapping_justification: >-
      MONDO:0019015 (omphalocele) is the disease term for this entry; it lists
      Orphanet:660, NCIT:C98997, and ICD-10 Q79.2 cross-references.
classifications:
  harrisons_chapter:
  - classification_value: GASTROINTESTINAL
    evidence:
    - reference: PMID:40150018
      reference_title: "Omphalocele and Associated Anomalies: Exploring Pulmonary Development and Genetic Correlations-A Literature Review."
      supports: SUPPORT
      evidence_source: HUMAN_CLINICAL
      snippet: "Omphalocele is a rare congenital abdominal wall defect, occurring in approximately 3.38 per 10,000 pregnancies. It is characterized by the herniation of abdominal organs through the base of the umbilical cord, enclosed by a peritoneal sac."
      explanation: >-
        Omphalocele is a congenital abdominal wall defect characterized by
        herniation of abdominal organs through the base of the umbilical cord.
  - classification_value: GENETICS_ENVIRONMENT_DISEASE
    evidence:
    - reference: PMID:34392395
      reference_title: "Omphalocele: national current birth prevalence and survival."
      supports: SUPPORT
      evidence_source: HUMAN_CLINICAL
      snippet: "About 62% of the cases had associated malformations and/or genetic disorders; most common was ventricular septal defect."
      explanation: >-
        Over half of omphalocele cases occur with associated congenital
        malformations or genetic disorders.
inheritance:
- name: Chromosomal and Syndromic
  inheritance_term:
    preferred_term: Non-Mendelian inheritance
    term:
      id: HP:0001426
      label: Non-Mendelian inheritance
  description: >-
    Non-isolated and syndromic omphalocele follows the chromosomal or syndromic
    inheritance pattern of the underlying condition; chromosomal abnormalities
    (such as trisomy 18 and trisomy 13) and congenital syndromes account for a
    large fraction of cases.
  evidence:
  - reference: PMID:34392395
    reference_title: "Omphalocele: national current birth prevalence and survival."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "About 62% of the cases had associated malformations and/or genetic disorders; most common was ventricular septal defect."
    explanation: >-
      Supports the high proportion of omphalocele cases associated with genetic
      and chromosomal disorders.

has_subtypes:
- name: Isolated
  display_name: Isolated (non-syndromic) omphalocele
  description: >-
    Omphalocele occurring without associated major malformations, chromosomal
    abnormality, or recognized syndrome. Isolated cases have the most favorable
    prognosis, with high survival in the absence of chromosomal defects.
  evidence:
  - reference: PMID:32131131
    reference_title: "Omphalocele in Finland from 1993 to 2014: Trends, Prevalence, Mortality, and Associated Malformations-A Population-Based Study."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "Total 1-year survival rates for isolated omphalocele, cases with multiple anomalies and neonates with chromosomal defects were 80, 88, and 17%, respectively."
    explanation: >-
      Distinguishes isolated omphalocele from cases with multiple anomalies or
      chromosomal defects and quantifies its higher 1-year survival rate.
- name: Syndromic
  display_name: Syndromic / chromosomal omphalocele
  description: >-
    Omphalocele occurring as part of a recognized congenital syndrome or
    chromosomal abnormality (such as trisomy 18, trisomy 13, or
    Beckwith-Wiedemann syndrome). Carries substantially worse prognosis, driven
    by the associated anomalies and chromosomal or syndromic diagnosis.
  evidence:
  - reference: PMID:39576336
    reference_title: "Omphalocele prevalence and co-occurring malformations: a nationwide register-based study of Danish live births in 1997-2021."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "Over one-half (53.7%) presented with one or more major malformations, and an additional 17.0% were diagnosed with a syndrome."
    explanation: >-
      Documents the syndromic and malformation-associated subgroup in a
      nationwide birth cohort.
  - reference: PMID:40150018
    reference_title: "Omphalocele and Associated Anomalies: Exploring Pulmonary Development and Genetic Correlations-A Literature Review."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "While omphalocele can occur as an isolated anomaly, it is more commonly associated with congenital syndromes and structural abnormalities."
    explanation: >-
      Confirms that omphalocele is commonly associated with congenital syndromes
      and structural abnormalities.
- name: Giant
  display_name: Giant omphalocele
  description: >-
    Anatomic size and severity stratum (which can occur in either isolated or
    syndromic omphalocele) characterized by viscero-abdominal disproportion
    that prevents primary fascial closure and predisposes to pulmonary
    hypoplasia and pulmonary hypertension.
  evidence:
  - reference: PMID:40389219
    reference_title: "European Paediatric Surgeons' Association Consensus Statement on the Management of Giant Omphalocele."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "Giant omphalocele is appropriately defined as viscero-abdominal disproportion preventing primary closure."
    explanation: >-
      Provides the European Paediatric Surgeons' Association consensus
      definition of giant omphalocele.

pathophysiology:
- name: Ventral Body Wall Closure Failure
  description: >-
    The primary developmental lesion in omphalocele is failure to complete
    normal ventral body wall formation at the umbilical region. During normal
    embryogenesis the lateral, cephalic, and caudal body folds migrate ventrally
    and fuse at the umbilical ring; failure of this morphogenetic process leaves
    a central defect through which abdominal viscera herniate into the base of
    the umbilical cord, covered by a membranous (peritoneum/Wharton's
    jelly/amnion) sac. This distinguishes omphalocele from gastroschisis (a
    paraumbilical defect without a sac).
  locations:
  - preferred_term: abdominal wall
    term:
      id: UBERON:0003697
      label: abdominal wall
  - preferred_term: umbilical cord
    term:
      id: UBERON:0002331
      label: umbilical cord
  cell_types:
  - preferred_term: Body wall mesenchymal cell
    term:
      id: CL:0000134
      label: mesenchymal stem cell
  - preferred_term: Body wall fibroblast
    term:
      id: CL:0000057
      label: fibroblast
  biological_processes:
  - preferred_term: Embryonic body morphogenesis (ventral body wall closure)
    term:
      id: GO:0010172
      label: embryonic body morphogenesis
    modifier: ABNORMAL
  - preferred_term: Mesenchymal cell migration (body-fold migration)
    term:
      id: GO:0090497
      label: mesenchymal cell migration
    modifier: DECREASED
  - preferred_term: Umbilical cord morphogenesis
    term:
      id: GO:0036304
      label: umbilical cord morphogenesis
    modifier: ABNORMAL
  evidence:
  - reference: PMID:38021990
    reference_title: "Enhancing Omphalocele Care: Navigating Complications and Innovative Treatment Approaches."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "Omphalocele refers to the herniation of abdominal contents through a defect in the abdominal wall at the umbilicus with or without the presence of a sac."
    explanation: >-
      Review defining omphalocele as herniation of abdominal contents through a
      ventral abdominal wall defect at the umbilicus, the anatomic consequence
      of failed ventral body wall closure.
  - reference: PMID:37726736
    reference_title: "Ultrasonographic characteristics, genetic features, and maternal and fetal outcomes in fetuses with omphalocele in China: a single tertiary center study."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "Patients with omphalocele, a midline abdominal wall defect at the umbilical cord base, have a low survival rate."
    explanation: >-
      Confirms the midline umbilical-base location of the abdominal wall defect
      that defines omphalocele.
  downstream:
  - target: Midgut Herniation and Viscero-Abdominal Disproportion
    description: >-
      Failure of ventral body wall closure leaves an open umbilical-ring defect
      through which abdominal viscera herniate into the membrane-covered sac.
    evidence:
    - reference: PMID:38021990
      reference_title: "Enhancing Omphalocele Care: Navigating Complications and Innovative Treatment Approaches."
      supports: SUPPORT
      evidence_source: HUMAN_CLINICAL
      snippet: "Omphalocele refers to the herniation of abdominal contents through a defect in the abdominal wall at the umbilicus with or without the presence of a sac."
      explanation: >-
        Supports that the abdominal wall defect at the umbilicus results in
        herniation of abdominal contents.
  - target: Omphalocele (ventral abdominal wall defect)
    description: >-
      Incomplete ventral abdominal wall closure directly manifests as the
      congenital omphalocele defect at the base of the umbilical cord.
    evidence:
    - reference: PMID:37726736
      reference_title: "Ultrasonographic characteristics, genetic features, and maternal and fetal outcomes in fetuses with omphalocele in China: a single tertiary center study."
      supports: SUPPORT
      evidence_source: HUMAN_CLINICAL
      snippet: "Patients with omphalocele, a midline abdominal wall defect at the umbilical cord base, have a low survival rate."
      explanation: >-
        Directly links the midline umbilical-base defect to the clinical
        omphalocele phenotype.
- name: Midgut Herniation and Viscero-Abdominal Disproportion
  description: >-
    Abdominal viscera - intestine and, in large/giant defects, the liver -
    herniate through the body wall defect into the sac. In normal development a
    physiologic midgut herniation occurs at ~6-10 weeks' gestation and returns
    to the abdominal cavity; persistence/failure of this return contributes to
    the pathologic herniation. The resulting reduction in intra-abdominal domain
    produces viscero-abdominal disproportion, which both complicates surgical
    reduction (risk of abdominal compartment syndrome) and, in giant defects,
    constrains thoraco-abdominal development.
  locations:
  - preferred_term: abdominal wall
    term:
      id: UBERON:0003697
      label: abdominal wall
  - preferred_term: liver
    term:
      id: UBERON:0002107
      label: liver
  cell_types:
  - preferred_term: Hepatocyte (herniated liver)
    term:
      id: CL:0000182
      label: hepatocyte
  biological_processes:
  - preferred_term: Midgut development
    term:
      id: GO:0007494
      label: midgut development
    modifier: ABNORMAL
  evidence:
  - reference: PMID:38021990
    reference_title: "Enhancing Omphalocele Care: Navigating Complications and Innovative Treatment Approaches."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "Omphalocele refers to the herniation of abdominal contents through a defect in the abdominal wall at the umbilicus with or without the presence of a sac."
    explanation: >-
      Supports herniation of abdominal contents (midgut, and in large defects
      liver) through the umbilical defect; the abstract does not separately
      quantify viscero-abdominal disproportion.
  - reference: PMID:40150018
    reference_title: "Omphalocele and Associated Anomalies: Exploring Pulmonary Development and Genetic Correlations-A Literature Review."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "giant omphaloceles are frequently linked to lung hypoplasia, as reduced intra-abdominal space restricts fetal lung expansion"
    explanation: >-
      Supports that reduced intra-abdominal space (viscero-abdominal
      disproportion) in giant omphalocele restricts fetal development.
  downstream:
  - target: Pulmonary Hypoplasia
    description: >-
      Viscero-abdominal disproportion in large/giant defects reduces the
      intra-abdominal domain and constrains thoraco-abdominal development,
      restricting fetal lung expansion.
    evidence:
    - reference: PMID:40150018
      reference_title: "Omphalocele and Associated Anomalies: Exploring Pulmonary Development and Genetic Correlations-A Literature Review."
      supports: SUPPORT
      evidence_source: HUMAN_CLINICAL
      snippet: "giant omphaloceles are frequently linked to lung hypoplasia, as reduced intra-abdominal space restricts fetal lung expansion, leading to structural lung abnormalities and increased pulmonary vascular resistance."
      explanation: >-
        Supports the causal link from reduced intra-abdominal space in giant
        omphalocele to restricted fetal lung expansion and lung hypoplasia.
- name: Pulmonary Hypoplasia
  description: >-
    In large/giant omphalocele the reduced intra-abdominal domain and abnormal
    thoraco-abdominal dynamics constrain fetal lung expansion, producing
    pulmonary hypoplasia with structural lung and vascular developmental
    abnormalities.
  locations:
  - preferred_term: lung
    term:
      id: UBERON:0002048
      label: lung
  biological_processes:
  - preferred_term: Lung development
    term:
      id: GO:0030324
      label: lung development
    modifier: DECREASED
  evidence:
  - reference: PMID:40150018
    reference_title: "Omphalocele and Associated Anomalies: Exploring Pulmonary Development and Genetic Correlations-A Literature Review."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "giant omphaloceles are frequently linked to lung hypoplasia, as reduced intra-abdominal space restricts fetal lung expansion, leading to structural lung abnormalities and increased pulmonary vascular resistance."
    explanation: >-
      Supports the mechanistic link from restricted fetal lung expansion to
      pulmonary hypoplasia and structural lung abnormalities.
  downstream:
  - target: Pulmonary hypoplasia
    description: >-
      Restricted fetal thoracic and intra-abdominal space directly impairs lung
      growth, causing clinical pulmonary hypoplasia.
    evidence:
    - reference: PMID:40150018
      reference_title: "Omphalocele and Associated Anomalies: Exploring Pulmonary Development and Genetic Correlations-A Literature Review."
      supports: SUPPORT
      evidence_source: HUMAN_CLINICAL
      snippet: "Among its most significant complications, pulmonary hypoplasia (PH) and pulmonary hypertension (PPH) have been shown to negatively impact neonatal prognosis."
      explanation: >-
        Supports pulmonary hypoplasia as a direct downstream complication.
  - target: Pulmonary Hypertension
    description: >-
      Structural lung hypoplasia and impaired pulmonary vascular development in
      giant omphalocele lead to increased pulmonary vascular resistance and
      pulmonary hypertension.
    evidence:
    - reference: PMID:40150018
      reference_title: "Omphalocele and Associated Anomalies: Exploring Pulmonary Development and Genetic Correlations-A Literature Review."
      supports: SUPPORT
      evidence_source: HUMAN_CLINICAL
      snippet: "giant omphaloceles are frequently linked to lung hypoplasia, as reduced intra-abdominal space restricts fetal lung expansion, leading to structural lung abnormalities and increased pulmonary vascular resistance."
      explanation: >-
        Links lung hypoplasia and structural lung abnormalities to increased
        pulmonary vascular resistance.
  - target: Respiratory insufficiency
    description: >-
      Pulmonary hypoplasia directly impairs neonatal gas exchange and causes
      severe respiratory insufficiency.
    evidence:
    - reference: PMID:40150018
      reference_title: "Omphalocele and Associated Anomalies: Exploring Pulmonary Development and Genetic Correlations-A Literature Review."
      supports: SUPPORT
      evidence_source: HUMAN_CLINICAL
      snippet: "Severe respiratory insufficiency, particularly due to pulmonary hypoplasia and pulmonary hypertension, significantly increases neonatal morbidity and mortality."
      explanation: >-
        Directly links pulmonary hypoplasia to severe neonatal respiratory
        insufficiency.
- name: Pulmonary Hypertension
  description: >-
    Impaired pulmonary vascular development and structural lung hypoplasia in
    giant omphalocele elevate pulmonary vascular resistance, producing neonatal
    pulmonary hypertension and hypoxemic respiratory distress.
  locations:
  - preferred_term: lung
    term:
      id: UBERON:0002048
      label: lung
  cell_types:
  - preferred_term: Pulmonary artery endothelial cell
    term:
      id: CL:1001568
      label: pulmonary artery endothelial cell
  - preferred_term: Pulmonary arterial smooth muscle cell
    term:
      id: CL:0002591
      label: smooth muscle cell of the pulmonary artery
  biological_processes:
  - preferred_term: Pulmonary vasculature development
    term:
      id: GO:0001944
      label: vasculature development
    modifier: ABNORMAL
  evidence:
  - reference: PMID:40150018
    reference_title: "Omphalocele and Associated Anomalies: Exploring Pulmonary Development and Genetic Correlations-A Literature Review."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "Among its most significant complications, pulmonary hypoplasia (PH) and pulmonary hypertension (PPH) have been shown to negatively impact neonatal prognosis. These conditions result from impaired pulmonary vascular development, leading to respiratory distress and hypoxemia."
    explanation: >-
      Directly supports pulmonary hypertension arising from impaired pulmonary
      vascular development in omphalocele.
  downstream:
  - target: Pulmonary hypertension
    description: >-
      Impaired pulmonary vascular development and elevated pulmonary vascular
      resistance manifest clinically as neonatal pulmonary hypertension.
    evidence:
    - reference: PMID:40150018
      reference_title: "Omphalocele and Associated Anomalies: Exploring Pulmonary Development and Genetic Correlations-A Literature Review."
      supports: SUPPORT
      evidence_source: HUMAN_CLINICAL
      snippet: "Among its most significant complications, pulmonary hypoplasia (PH) and pulmonary hypertension (PPH) have been shown to negatively impact neonatal prognosis."
      explanation: >-
        Supports pulmonary hypertension as a major downstream clinical
        manifestation.
  - target: Respiratory insufficiency
    description: >-
      Elevated pulmonary vascular resistance and pulmonary hypertension cause
      hypoxemia and severe neonatal respiratory insufficiency.
    evidence:
    - reference: PMID:40150018
      reference_title: "Omphalocele and Associated Anomalies: Exploring Pulmonary Development and Genetic Correlations-A Literature Review."
      supports: SUPPORT
      evidence_source: HUMAN_CLINICAL
      snippet: "Severe respiratory insufficiency, particularly due to pulmonary hypoplasia and pulmonary hypertension, significantly increases neonatal morbidity and mortality."
      explanation: >-
        Directly links pulmonary hypertension to severe respiratory
        insufficiency.

phenotypes:
- category: Physical
  name: Omphalocele (ventral abdominal wall defect)
  description: >-
    Core defining phenotype: a midline abdominal wall defect at the umbilicus
    with sac-covered herniation of abdominal viscera.
  frequency: OBLIGATE
  phenotype_term:
    preferred_term: Omphalocele
    term:
      id: HP:0001539
      label: Omphalocele
    onset:
      onset_category: CONGENITAL
  evidence:
  - reference: PMID:38021990
    reference_title: "Enhancing Omphalocele Care: Navigating Complications and Innovative Treatment Approaches."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "Omphalocele refers to the herniation of abdominal contents through a defect in the abdominal wall at the umbilicus with or without the presence of a sac."
    explanation: Defines the core omphalocele phenotype.
- category: Physical
  name: Congenital heart defects
  description: >-
    Cardiac anomalies are among the most frequent associated malformations in
    omphalocele and are an important prognostic determinant. In one postnatal
    cohort, cardiac anomalies were identified in 37.5% of omphalocele patients.
  frequency: FREQUENT
  phenotype_term:
    preferred_term: Abnormal heart morphology
    term:
      id: HP:0001627
      label: Abnormal heart morphology
  evidence:
  - reference: PMID:37189937
    reference_title: "Additional Anomalies in Children with Gastroschisis and Omphalocele: A Retrospective Cohort Study."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "in patients with omphalocele, cardiac anomalies were most identified (n = 15, 37.5%)"
    explanation: >-
      Supports congenital heart defects as the most common associated anomaly in
      omphalocele, present in 37.5% of the cohort.
- category: Physical
  name: Ventricular septal defect
  description: >-
    Ventricular septal defect was the single most common associated
    malformation in the Swedish national omphalocele cohort.
  phenotype_term:
    preferred_term: Ventricular septal defect
    term:
      id: HP:0001629
      label: Ventricular septal defect
  evidence:
  - reference: PMID:34392395
    reference_title: "Omphalocele: national current birth prevalence and survival."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "About 62% of the cases had associated malformations and/or genetic disorders; most common was ventricular septal defect."
    explanation: >-
      Supports ventricular septal defect as the most common associated
      malformation in a national cohort.
- category: Physical
  name: Pulmonary hypoplasia
  description: >-
    Pulmonary hypoplasia is an important complication, especially in giant
    omphalocele, and is linked to worse neonatal respiratory outcomes.
  subtype: Giant
  phenotype_term:
    preferred_term: Pulmonary hypoplasia
    term:
      id: HP:0002089
      label: Pulmonary hypoplasia
  evidence:
  - reference: PMID:40150018
    reference_title: "Omphalocele and Associated Anomalies: Exploring Pulmonary Development and Genetic Correlations-A Literature Review."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "Among its most significant complications, pulmonary hypoplasia (PH) and pulmonary hypertension (PPH) have been shown to negatively impact neonatal prognosis."
    explanation: Supports pulmonary hypoplasia as a significant complication.
- category: Physical
  name: Pulmonary hypertension
  description: >-
    Pulmonary hypertension occurs in infants with giant omphalocele and
    contributes to respiratory morbidity and mortality.
  subtype: Giant
  phenotype_term:
    preferred_term: Pulmonary hypertension
    term:
      id: HP:0002092
      label: Pulmonary arterial hypertension
  evidence:
  - reference: PMID:40150018
    reference_title: "Omphalocele and Associated Anomalies: Exploring Pulmonary Development and Genetic Correlations-A Literature Review."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "Severe respiratory insufficiency, particularly due to pulmonary hypoplasia and pulmonary hypertension, significantly increases neonatal morbidity and mortality."
    explanation: >-
      Supports pulmonary hypertension as a contributor to neonatal morbidity and
      mortality.
- category: Physical
  name: Respiratory insufficiency
  description: >-
    Severe respiratory insufficiency is a major morbidity in giant omphalocele,
    particularly with pulmonary hypoplasia/hypertension.
  subtype: Giant
  phenotype_term:
    preferred_term: Respiratory insufficiency
    term:
      id: HP:0002093
      label: Respiratory insufficiency
  evidence:
  - reference: PMID:40150018
    reference_title: "Omphalocele and Associated Anomalies: Exploring Pulmonary Development and Genetic Correlations-A Literature Review."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "Severe respiratory insufficiency, particularly due to pulmonary hypoplasia and pulmonary hypertension, significantly increases neonatal morbidity and mortality."
    explanation: Supports severe respiratory insufficiency as a major morbidity.
- category: Physical
  name: Feeding difficulties
  description: >-
    Feeding difficulty is a recognized sequela, particularly in giant
    omphalocele; management studies track time to full enteral feeds.
  subtype: Giant
  phenotype_term:
    preferred_term: Feeding difficulties
    term:
      id: HP:0011968
      label: Feeding difficulties
  evidence:
  - reference: PMID:38376641
    reference_title: "A case series of successfully managing exomphalos major with awake graduated compression dressing and early enteral feeding."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "The average time taken to reach full feeds was 1 week; only one patient required parenteral nutrition."
    explanation: >-
      A case series of exomphalos major tracks time to full feeds, reflecting
      feeding difficulty as a clinically relevant sequela.

genetic:
- name: Chromosomal aneuploidy (trisomy 13, 18, 21)
  inheritance:
  - name: Chromosomal
    inheritance_term:
      preferred_term: Non-Mendelian inheritance
      term:
        id: HP:0001426
        label: Non-Mendelian inheritance
  features: >-
    Omphalocele is frequently associated with chromosomal aneuploidy, most
    commonly trisomy 13, trisomy 18, and trisomy 21. Across population cohorts,
    the chromosomal-abnormality subgroup carries markedly elevated mortality;
    in the Swedish national cohort about 62% of cases had associated
    malformations and/or genetic disorders.
  subtype: Syndromic
  evidence:
  - reference: PMID:34392395
    reference_title: "Omphalocele: national current birth prevalence and survival."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "About 62% of the cases had associated malformations and/or genetic disorders; most common was ventricular septal defect."
    explanation: >-
      Supports the high proportion of omphalocele cases with associated genetic
      disorders, including chromosomal abnormalities.
- name: Associated chromosomal abnormalities (population estimate)
  inheritance:
  - name: Chromosomal
    inheritance_term:
      preferred_term: Non-Mendelian inheritance
      term:
        id: HP:0001426
        label: Non-Mendelian inheritance
  features: >-
    In a Finnish population-based study, chromosomal abnormalities were the most
    common associated anomaly (9.3%), and 1-year survival was far lower for
    neonates with chromosomal defects (17%) than for isolated cases (80%).
  evidence:
  - reference: PMID:32131131
    reference_title: "Omphalocele in Finland from 1993 to 2014: Trends, Prevalence, Mortality, and Associated Malformations-A Population-Based Study."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "most commonly chromosomal abnormalities (9.3%), heart defects (6.3%), central nervous system anomalies (3.0%)"
    explanation: >-
      Supports chromosomal abnormalities as the most common associated anomaly
      in a population-based omphalocele cohort.
- name: Monogenic variants in selected non-isolated cases
  features: >-
    When prenatal karyotype and chromosomal microarray are normal, whole exome
    sequencing can identify monogenic variants in selected non-isolated cases. In
    a Chinese prenatal cohort, WES of six karyotype/CMA-normal non-isolated cases
    revealed one pathogenic and two suspected pathogenic variants.
  subtype: Syndromic
  evidence:
  - reference: PMID:37726736
    reference_title: "Ultrasonographic characteristics, genetic features, and maternal and fetal outcomes in fetuses with omphalocele in China: a single tertiary center study."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "Six nonisolated cases had normal CMA results and conventional karyotype tests, and further WES examination revealed one pathogenic variant and two suspected pathogenic variants."
    explanation: >-
      Supports a monogenic contribution detectable by WES in selected
      non-isolated omphalocele cases with normal karyotype/CMA.

prevalence:
- population: Danish live births (1997-2021)
  measure_type: BIRTH_PREVALENCE
  prevalence_class: BAND_1_9_PER_100000
  rate_per_100000: 9.8
  notes: >-
    Danish nationwide live-birth register study: omphalocele birth prevalence of
    0.98 per 10,000 infants (95% CI 0.83-1.15). Over half (53.7%) had one or more
    major malformations and an additional 17.0% had a diagnosed syndrome.
  evidence:
  - reference: PMID:39576336
    reference_title: "Omphalocele prevalence and co-occurring malformations: a nationwide register-based study of Danish live births in 1997-2021."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "Among 1,498,685 live births, 147 infants with omphalocele were identified, yielding a combined and stable prevalence (per 10,000 infants) of 0.98 (95% CI 0.83-1.15). Over one-half (53.7%) presented with one or more major malformations, and an additional 17.0% were diagnosed with a syndrome."
    explanation: >-
      Provides nationwide live-birth prevalence and the proportion of cases with
      co-occurring major malformations and syndromes.
- population: Finnish births (1993-2014, including terminations)
  measure_type: BIRTH_PREVALENCE
  prevalence_class: BAND_1_5_PER_10000
  rate_per_100000: 19.6
  notes: >-
    Finnish population-based register study including terminations: total
    prevalence 4.71 per 10,000 births, birth prevalence 1.96 per 10,000, with
    55% of pregnancies terminated.
  evidence:
  - reference: PMID:32131131
    reference_title: "Omphalocele in Finland from 1993 to 2014: Trends, Prevalence, Mortality, and Associated Malformations-A Population-Based Study."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "Birth prevalence in Finland was 1.96 per 10,000 births with no consistent trend over time. However, total prevalence was much higher (4.71/10,000) because more than half of these families chose option for the termination of pregnancy."
    explanation: >-
      Provides total and birth prevalence including terminations, and the high
      termination rate.

diagnosis:
- name: Prenatal ultrasonography
  description: >-
    Prenatal ultrasound identifies the midline ventral abdominal wall defect at
    the base of the umbilical cord, characterizes herniated contents (such as
    liver), and screens for co-occurring structural malformations to classify
    isolated versus non-isolated omphalocele.
  results: >-
    Demonstration of a membrane-covered midline umbilical-base abdominal wall
    defect and assessment for associated anomalies.
  diagnosis_term:
    preferred_term: Fetal Ultrasound Imaging
    term:
      id: NCIT:C222238
      label: Fetal Ultrasound Imaging
  evidence:
  - reference: PMID:37726736
    reference_title: "Ultrasonographic characteristics, genetic features, and maternal and fetal outcomes in fetuses with omphalocele in China: a single tertiary center study."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "Among the 120 fetuses, 27 were diagnosed with isolated omphalocele and 93 with nonisolated omphalocele using prenatal ultrasonography."
    explanation: >-
      Establishes prenatal ultrasonography as the primary modality for
      detecting associated malformations and classifying omphalocele.
- name: Karyotyping and chromosomal microarray analysis
  description: >-
    Conventional karyotyping combined with chromosomal microarray analysis (CMA)
    is recommended for all fetuses diagnosed with omphalocele to identify
    aneuploidies and pathogenic copy-number variants.
  results: >-
    Detection of chromosomal aneuploidy or submicroscopic copy-number variants
    in syndromic/chromosomal omphalocele.
  diagnosis_term:
    preferred_term: Microarray Analysis
    term:
      id: NCIT:C18477
      label: Microarray Analysis
  evidence:
  - reference: PMID:37726736
    reference_title: "Ultrasonographic characteristics, genetic features, and maternal and fetal outcomes in fetuses with omphalocele in China: a single tertiary center study."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "Routine karyotyping with CMA testing should be provided for fetuses with omphalocele. WES is an option if karyotype and CMA tests are normal."
    explanation: >-
      Supports routine prenatal karyotyping and chromosomal microarray testing
      for fetuses with omphalocele.
- name: Whole exome sequencing
  description: >-
    Whole exome sequencing (WES) is used as a reflex diagnostic test in
    non-isolated omphalocele when conventional karyotyping and chromosomal
    microarray analysis are normal.
  results: >-
    Identification of pathogenic or likely pathogenic single-gene variants in
    non-isolated omphalocele.
  diagnosis_term:
    preferred_term: Whole Exome Sequencing
    term:
      id: NCIT:C101295
      label: Whole Exome Sequencing
  evidence:
  - reference: PMID:37726736
    reference_title: "Ultrasonographic characteristics, genetic features, and maternal and fetal outcomes in fetuses with omphalocele in China: a single tertiary center study."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "Six nonisolated cases had normal CMA results and conventional karyotype tests, and further WES examination revealed one pathogenic variant and two suspected pathogenic variants."
    explanation: >-
      Demonstrates diagnostic yield of WES in non-isolated omphalocele with
      normal karyotype and CMA.

differential_diagnoses:
- name: Gastroschisis
  description: >-
    Congenital paraumbilical abdominal wall defect with evisceration of bowel
    lacking a covering membranous sac and displaying a distinct pattern of
    associated anomalies (predominantly intestinal rather than cardiac or
    chromosomal).
  distinguishing_features:
  - Paraumbilical defect without a covering peritoneal/amniotic sac, whereas omphalocele occurs at the umbilical cord base with a sac.
  - Associated anomalies in gastroschisis are predominantly intestinal, whereas cardiac and chromosomal anomalies predominate in omphalocele.
  evidence:
  - reference: PMID:37189937
    reference_title: "Additional Anomalies in Children with Gastroschisis and Omphalocele: A Retrospective Cohort Study."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "In patients with gastroschisis, intestinal anomalies were most identified (n = 13, 15.9%), whereas, in patients with omphalocele, cardiac anomalies were most identified (n = 15, 37.5%)."
    explanation: >-
      Contrasts the anomaly profiles of gastroschisis and omphalocele in a
      comparative cohort study.

progression:
- phase: Neonatal outcome (chromosome/anomaly dependent)
  notes: >-
    Omphalocele is congenital and frequently diagnosed prenatally by ultrasound.
    Prognosis is driven primarily by associated anomalies and chromosomal/
    syndromic diagnoses rather than the abdominal wall defect alone; in the
    absence of chromosomal defects survival is reasonably good. In the Finnish
    cohort, 1-year survival was 80% for isolated omphalocele versus 17% for
    neonates with chromosomal defects.
  evidence:
  - reference: PMID:32131131
    reference_title: "Omphalocele in Finland from 1993 to 2014: Trends, Prevalence, Mortality, and Associated Malformations-A Population-Based Study."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "Total 1-year survival rates for isolated omphalocele, cases with multiple anomalies and neonates with chromosomal defects were 80, 88, and 17%, respectively."
    explanation: >-
      Quantifies the large survival difference between isolated and
      chromosomally abnormal omphalocele.
  - reference: PMID:32131131
    reference_title: "Omphalocele in Finland from 1993 to 2014: Trends, Prevalence, Mortality, and Associated Malformations-A Population-Based Study."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "In the absence of chromosomal defects, survival is reasonably good."
    explanation: >-
      Supports good survival when chromosomal defects are absent.

treatments:
- name: Primary surgical closure
  description: >-
    Definitive early operative reduction of herniated viscera and closure of the
    abdominal wall defect. Best suited to small omphaloceles or cases without
    major viscero-abdominal disproportion; urgent reduction can dangerously raise
    intra-abdominal pressure and precipitate abdominal compartment syndrome.
  therapeutic_modality: SURGERY
  treatment_term:
    preferred_term: surgical procedure
    term:
      id: NCIT:C15329
      label: Surgical Procedure
  target_mechanisms:
  - target: Ventral Body Wall Closure Failure
    treatment_effect: RESTORES
    description: >-
      Operative fascial repair directly closes the congenital ventral abdominal
      wall defect in patients without prohibitive viscero-abdominal
      disproportion.
    evidence:
    - reference: PMID:40389219
      reference_title: "European Paediatric Surgeons' Association Consensus Statement on the Management of Giant Omphalocele."
      supports: SUPPORT
      evidence_source: HUMAN_CLINICAL
      directness: INDIRECT
      snippet: "Giant omphalocele is appropriately defined as viscero-abdominal disproportion preventing primary closure."
      explanation: >-
        Supports primary surgical closure as the standard restorative approach
        when viscero-abdominal disproportion does not prevent primary closure.
  evidence:
  - reference: PMID:40389219
    reference_title: "European Paediatric Surgeons' Association Consensus Statement on the Management of Giant Omphalocele."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "Giant omphalocele is appropriately defined as viscero-abdominal disproportion preventing primary closure."
    explanation: >-
      The EUPSA consensus defines giant omphalocele by viscero-abdominal
      disproportion that precludes primary closure, indicating primary closure
      is the approach for non-giant defects.
- name: Staged / traction-assisted closure
  description: >-
    Staged reduction (e.g., silo) or vertical traction-assisted staged closure
    is used when primary closure is unsafe because of a large defect, liver
    herniation, or marked viscero-abdominal disproportion. A prospective device
    series achieved complete fascial closure in all 16 patients (10 giant
    omphalocele, 6 gastroschisis) with no abdominal compartment syndrome.
  therapeutic_modality: SURGERY
  treatment_term:
    preferred_term: surgical procedure
    term:
      id: NCIT:C15329
      label: Surgical Procedure
  target_mechanisms:
  - target: Midgut Herniation and Viscero-Abdominal Disproportion
    treatment_effect: RESTORES
    description: >-
      Gradual staged or vertical-traction reduction accommodates herniated
      viscera and expands the intra-abdominal domain before definitive fascial
      closure.
    evidence:
    - reference: PMID:38960901
      reference_title: "Use of a new vertical traction device for early traction-assisted staged closure of congenital abdominal wall defects: a prospective series of 16 patients."
      supports: SUPPORT
      evidence_source: HUMAN_CLINICAL
      snippet: "Complete fascial closure was achieved after a median time of 7 days (range 4-22) in GOC and 5 days (range 4-11) in GS."
      explanation: >-
        Demonstrates that traction-assisted staged reduction overcomes
        viscero-abdominal disproportion to achieve complete fascial closure.
  evidence:
  - reference: PMID:38960901
    reference_title: "Use of a new vertical traction device for early traction-assisted staged closure of congenital abdominal wall defects: a prospective series of 16 patients."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "Complete fascial closure was achieved after a median time of 7 days (range 4-22) in GOC and 5 days (range 4-11) in GS."
    explanation: >-
      Supports traction-assisted staged closure achieving complete fascial
      closure in giant omphalocele and gastroschisis.
- name: Conservative "paint and wait" management
  description: >-
    Non-operative topical epithelialization of the intact sac, recommended when
    anatomical constraints or high surgical risk preclude primary closure
    (especially giant omphalocele with liver exteriorization and/or pulmonary
    hypoplasia/hypertension). Common painting agents include povidone-iodine and
    silver sulfadiazine. Later definitive ventral hernia repair is often needed.
  therapeutic_modality: SMALL_MOLECULE
  treatment_term:
    preferred_term: topical pharmacotherapy
    term:
      id: NCIT:C15986
      label: Pharmacotherapy
  target_mechanisms:
  - target: Midgut Herniation and Viscero-Abdominal Disproportion
    treatment_effect: MODULATES
    description: >-
      Topical escharotic therapy epithelializes the intact sac while deferring
      visceral reduction and fascial closure until later, avoiding acute
      increases in intra-abdominal pressure when viscero-abdominal
      disproportion precludes primary surgical closure.
    evidence:
    - reference: PMID:40389219
      reference_title: "European Paediatric Surgeons' Association Consensus Statement on the Management of Giant Omphalocele."
      supports: SUPPORT
      evidence_source: HUMAN_CLINICAL
      snippet: "the \"paint and wait\" approach is recommended when anatomical constraints or high surgical risk preclude primary closure. Common painting agents include povidone-iodine and silver sulfadiazine"
      explanation: >-
        Supports topical escharotic sac management when anatomical constraints
        (viscero-abdominal disproportion) or surgical risk preclude primary
        closure.
  evidence:
  - reference: PMID:40389219
    reference_title: "European Paediatric Surgeons' Association Consensus Statement on the Management of Giant Omphalocele."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "the \"paint and wait\" approach is recommended when anatomical constraints or high surgical risk preclude primary closure. Common painting agents include povidone-iodine and silver sulfadiazine"
    explanation: >-
      EUPSA consensus recommends paint-and-wait conservative topical management
      when primary closure is precluded.
- name: Awake graduated compression dressing
  description: >-
    A bedside, awake gradual compression dressing technique for exomphalos major
    that reduces sac contents without general anaesthetic or respiratory
    compromise and permits simultaneous early enteral feeding.
  therapeutic_modality: OTHER
  treatment_term:
    preferred_term: supportive care
    term:
      id: NCIT:C15747
      label: Supportive Care
  target_mechanisms:
  - target: Midgut Herniation and Viscero-Abdominal Disproportion
    treatment_effect: RESTORES
    description: >-
      Gradual external compression reduces herniated sac contents without
      precipitating respiratory compromise.
    evidence:
    - reference: PMID:38376641
      reference_title: "A case series of successfully managing exomphalos major with awake graduated compression dressing and early enteral feeding."
      supports: SUPPORT
      evidence_source: HUMAN_CLINICAL
      snippet: "This case series describes a successful compression dressing technique that reduces sac content without the need for general anaesthetic or respiratory compromise, whereby simultaneous enteral feeding is tolerated."
      explanation: >-
        Demonstrates that awake graduated compression dressing reduces herniated
        sac contents without respiratory compromise.
  evidence:
  - reference: PMID:38376641
    reference_title: "A case series of successfully managing exomphalos major with awake graduated compression dressing and early enteral feeding."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "This case series describes a successful compression dressing technique that reduces sac content without the need for general anaesthetic or respiratory compromise, whereby simultaneous enteral feeding is tolerated."
    explanation: >-
      Supports awake graduated compression dressing as a conservative bedside
      reduction strategy for exomphalos major.
- name: Genetic counseling
  description: >-
    Genetic counseling addresses the high rate of associated chromosomal
    abnormalities and congenital syndromes in omphalocele and their prognostic
    and recurrence implications.
  therapeutic_modality: OTHER
  treatment_term:
    preferred_term: Genetic Counseling
    term:
      id: NCIT:C15240
      label: Genetic Counseling
  evidence:
  - reference: PMID:39576336
    reference_title: "Omphalocele prevalence and co-occurring malformations: a nationwide register-based study of Danish live births in 1997-2021."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "Over one-half (53.7%) presented with one or more major malformations, and an additional 17.0% were diagnosed with a syndrome."
    explanation: >-
      The high burden of co-occurring malformations and syndromes supports the
      role of genetic counseling.

references:
- reference: PMID:32131131
  title: "Omphalocele in Finland from 1993 to 2014: Trends, Prevalence, Mortality, and Associated Malformations-A Population-Based Study."
- reference: PMID:34392395
  title: "Omphalocele: national current birth prevalence and survival."
- reference: PMID:37189937
  title: "Additional Anomalies in Children with Gastroschisis and Omphalocele: A Retrospective Cohort Study."
- reference: PMID:37726736
  title: "Ultrasonographic characteristics, genetic features, and maternal and fetal outcomes in fetuses with omphalocele in China: a single tertiary center study."
- reference: PMID:38021990
  title: "Enhancing Omphalocele Care: Navigating Complications and Innovative Treatment Approaches."
- reference: PMID:38376641
  title: "A case series of successfully managing exomphalos major with awake graduated compression dressing and early enteral feeding."
- reference: PMID:38960901
  title: "Use of a new vertical traction device for early traction-assisted staged closure of congenital abdominal wall defects: a prospective series of 16 patients."
- reference: PMID:39576336
  title: "Omphalocele prevalence and co-occurring malformations: a nationwide register-based study of Danish live births in 1997-2021."
- reference: PMID:40150018
  title: "Omphalocele and Associated Anomalies: Exploring Pulmonary Development and Genetic Correlations-A Literature Review."
- reference: PMID:40389219
  title: "European Paediatric Surgeons' Association Consensus Statement on the Management of Giant Omphalocele."
datasets:
- accession: geo:GSE299253
  title: Hand1 gene replacement with Hand2 reveals overlap in function with unique occurrence of omphalocele and heart defects [scRNA-seq]
  description: The bHLH transcription factors HAND1 and HAND2 are expressed in partially overlapping patterns during development. Studies have established evidence for significant functional redundancy between HAND1 and HAND2. To test redundancy fully, we engineered a Hand1 allele where we directly replace the exons and intron with those of Hand2. Results show that 2% of Hand1Hand2/ Hand2 mice are viable, and fertile. The remaining Hand1Hand2/Hand2 embryos exhibit neonatal lethality due to omphalocele, ventricular septal defects and conduction anomalies.
  organism:
    preferred_term: mouse
    term:
      id: NCBITaxon:10090
      label: Mus musculus
  data_type: SINGLE_CELL_RNA_SEQ
  sample_count: 9
  publication: PMID:40960281
  notes: Identified by GEO DataSets index search for Omphalocele (scripts/discover_datasets.py); accession and metadata verified against NCBI E-utilities on 2026-08-01. Title, sample count, and organism are GEO's own values.
- accession: geo:GSE299579
  title: Hand1 gene replacement with Hand2 reveals overlap in function with unique occurrence of omphalocele and heart defects
  organism:
    preferred_term: mouse
    term:
      id: NCBITaxon:10090
      label: Mus musculus
  data_type: BULK_RNA_SEQ
  sample_count: 24
  notes: Identified by GEO DataSets index search for Omphalocele (scripts/discover_datasets.py); accession and metadata verified against NCBI E-utilities on 2026-08-01. Title, sample count, and organism are GEO's own values.
- accession: geo:GSE298742
  title: Hand1 gene replacement with Hand2 reveals overlap in function with unique occurrence of omphalocele and heart defects [Spatial Transcriptomics]
  data_type: SPATIAL_TRANSCRIPTOMICS
  description: The bHLH transcription factors HAND1 and HAND2 are expressed in partially overlapping patterns during development. Studies have established evidence for significant functional redundancy between HAND1 and HAND2. To test redundancy fully, we engineered a Hand1 allele where we directly replace the exons and intron with those of Hand2. Results show that 2% of Hand1Hand2/ Hand2 mice are viable, and fertile. The remaining Hand1Hand2/Hand2 embryos exhibit neonatal lethality due to omphalocele, ventricular septal defects and conduction anomalies.
  organism:
    preferred_term: mouse
    term:
      id: NCBITaxon:10090
      label: Mus musculus
  sample_count: 15
  notes: Identified by GEO DataSets index search for Omphalocele (scripts/discover_datasets.py); accession and metadata verified against NCBI E-utilities on 2026-08-01. Title, sample count, and organism are GEO's own values.

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References & Deep Research

References

10

PMID:32131131

Omphalocele in Finland from 1993 to 2014: Trends, Prevalence, Mortality, and Associated Malformations-A Population-Based Study.