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Hyperamylasaemia in paediatric inflammatory bowel disease: Aetiology, outcomes and genetic determinants

Fernando Vázquez López¹, Pranav Kesavan^2,3, Lynn K Win¹

¹Human Genetics and Genomic Medicine, University of Southampton, Southampton, UK.

Journal of Pediatric Gastroenterology and Nutrition

|April 27, 2026

Insights

Hyperamylasaemia is common in pediatric inflammatory bowel disease (IBD), linked to younger age, non-European ethnicity, and higher BMI. Elevated amylase levels often correlate with increased AMY gene copies and are usually benign.

Area of Science:

Gastroenterology
Genetics
Pediatrics

Background:

A subset of patients with inflammatory bowel disease (IBD) experience elevated serum amylase levels (hyperamylasaemia).
The underlying causes, clinical course, and genetic factors, such as amylase gene copy number variation (CNV), of hyperamylasaemia in pediatric IBD (pIBD) require further investigation.

Purpose of the Study:

To investigate the causes and clinical outcomes of hyperamylasaemia in pediatric IBD patients.
To determine the impact of amylase gene copy number variation (CNV) on serum amylase levels in this population using whole exome sequencing (WES).

Main Methods:

Retrospective analysis of 334 pediatric IBD patients diagnosed between 2015-2022.
Clinical characterization and follow-up of patients with hyperamylasaemia (amylase > 102 U/L) for at least 2 years.
Estimation of amylase gene CNV and correlation with serum amylase levels, with replication in an additional cohort of 554 patients.

Main Results:

Hyperamylasaemia was identified in 18.6% of pIBD patients, frequently at diagnosis.
Significant associations were found with younger age at diagnosis, non-European ethnicity, and high BMI.
Serum amylase levels positively correlated with AMY gene copy number, though CNV explained less than 10% of the variance.

Conclusions:

Hyperamylasaemia is a common finding in pediatric IBD, associated with specific demographic and clinical factors.
The majority of hyperamylasaemia cases in pIBD are benign and self-limiting.
Elevated amylase levels are strongly associated with increased copies of AMY genes in IBD patients.

Read full analysis

Abstract

Objectives:

A subset of patients with inflammatory bowel disease (IBD) develop hyperamylasaemia. This study examines its causes, clinical outcomes and the impact of amylase gene copy number variation (CNV) using whole exome sequencing (WES).

Methods:

We retrospectively analysed 334 patients with paediatric IBD (≤18 years, diagnosed 2015-2022) who were recruited to the Genetics of IBD Study-University Hospital Southampton. Patients with amylase levels above the laboratory's reference range (102 U/L) were identified, clinically characterised and followed for ≥2 years. Amylase gene CNV was estimated and correlated with serum amylase levels. Findings were replicated in an additional cohort of 554 paediatric and adult patients.

Results:

Hyperamylasaemia was found in 62/334 patients (18.6%), with 29% of these presenting at diagnosis. It was significantly associated with younger age at diagnosis (p = 0.044), non-European ethnicity (p = 0.013) and body mass index (BMI) > 91st centile (p = 0.0467). Hyperamylasaemia resolved in 77% of patients; in the majority (85%), spontaneously and in the remainder after medication withdrawal. One patient developed acute pancreatitis; another with ansa pancreatica had recurrent pancreatitis. Although AMY mean gene read counts positively correlated with median serum amylase levels in both cohorts (Primary pIBD cohort, p < 0.0001 for both AMY1 & AMY2; Replication cohort, p < 0.0001 for AMY1 & p = 0.0017 for AMY2), they explained <10% of the variance in amylase levels.

Conclusions:

Hyperamylasaemia is common in pIBD, associated with younger age, non-European ethnicity and higher BMI. Most cases are benign and self-limiting. Our findings confirm a strong association between elevated amylase and additional copies of AMY genes.

Keywords:

biomarkers gene copy number variation paediatric gastroenterology whole exome sequencing

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