| Clinical feature / phenotype | Phenotype type | Suggested HPO term(s) | Notes / frequency or context | Evidence source |
|---|---|---|---|---|
| Midline abdominal wall defect at umbilicus covered by sac (omphalocele/exomphalos) | Congenital structural anomaly | HP:0001539 Omphalocele | Core defining phenotype: herniation of abdominal contents through the umbilical insertion, typically sac-covered | (pqac-00000006, pqac-00000009) |
| Herniation of liver into sac | Congenital structural anomaly | HP:0012368 Herniation of the liver | Used clinically to distinguish larger/giant lesions; large lesions commonly involve liver herniation | (pqac-00000009, pqac-00000011) |
| Herniation of bowel/intestine into sac | Congenital structural anomaly | HP:0002240 Intestinal malrotation; HP:0033127 Abnormality of the intestine morphology | Bowel is commonly among herniated viscera; exact HPO for “bowel in sac” is not standard, so broader intestinal morphology terms may be needed in addition to HP:0001539 | (pqac-00000006, pqac-00000023) |
| Pulmonary hypoplasia | Respiratory structural anomaly | HP:0002089 Pulmonary hypoplasia | Important complication, especially in giant omphalocele; linked to worse neonatal respiratory outcomes and mortality | (pqac-00000000, pqac-00000003) |
| Pulmonary hypertension | Cardiopulmonary complication | HP:0002092 Pulmonary hypertension | Reported in infants with giant omphalocele and associated with respiratory morbidity | (pqac-00000000, pqac-00000003) |
| Congenital heart defects (overall) | Congenital structural anomaly | HP:0001627 Abnormal heart morphology | Cardiac anomalies are among the most frequent associated anomalies in omphalocele; 37.5% in one postnatal cohort of omphalocele patients | (pqac-00000011, pqac-00000012) |
| Ventricular septal defect | Congenital structural anomaly | HP:0001629 Ventricular septal defect | Most common associated malformation in Swedish national cohort | (pqac-00000026, pqac-00000027) |
| Atrial septal defect | Congenital structural anomaly | HP:0001631 Atrial septal defect | Common associated cardiac lesion, reported after VSD in Swedish cohort | (pqac-00000027) |
| Skeletal anomalies | Congenital structural anomaly | HP:0000924 Abnormality of the skeletal system | Prenatal cohort reported skeletal anomalies in 31.2% (38/120) of fetuses with omphalocele | (pqac-00000013, pqac-00000014) |
| Central nervous system anomalies | Congenital structural anomaly | HP:0000707 Abnormality of the nervous system | Prenatal cohort reported CNS malformations in 22.5% (27/120) | (pqac-00000013, pqac-00000014) |
| Feeding difficulties / delayed achievement of feeds | Functional / gastrointestinal phenotype | HP:0011968 Feeding difficulties in infancy | Feeding difficulty is a recognized sequela in giant omphalocele; management studies track time to full feeds | (pqac-00000002, pqac-00000023) |
| Respiratory insufficiency / respiratory distress | Clinical sign | HP:0002093 Respiratory insufficiency; HP:0002098 Respiratory distress | Severe respiratory insufficiency is a major morbidity in giant omphalocele, especially with pulmonary hypoplasia/hypertension | (pqac-00000000, pqac-00000002) |
| Gastroesophageal reflux disease (GERD) | Gastrointestinal symptom/disorder | HP:0002020 Gastroesophageal reflux | Reported as a later morbidity in giant omphalocele survivors | (pqac-00000003) |
| Neurodevelopmental delay | Neurodevelopmental phenotype | HP:0012758 Neurodevelopmental delay | Long-term neurodevelopmental issues are recognized in giant omphalocele survivors and in children with major associated anomalies | (pqac-00000002, pqac-00000014) |
| Autism spectrum disorder | Behavioral / neurodevelopmental phenotype | HP:0000729 Autism | Evidence mainly from giant omphalocele survivor cohorts rather than all omphalocele cases | (pqac-00000002) |


*Table: This table maps major clinical features of omphalocele to suggested HPO terms and summarizes the supporting evidence. It is useful for populating phenotype annotations in a disease knowledge base, especially for distinguishing core defects from common associated cardiopulmonary and neurodevelopmental complications.*