Because ALGS varies so much—even between family members with the same mutation—doctors use a "point system" for diagnosis. In 2026, a diagnosis is typically confirmed if a patient has three out of the five major clinical features:

1. Liver Disease: Cholestasis and bile duct paucity.

2. Heart Disease: Specifically pulmonary artery narrowing.

3. Skeletal Anomalies: Butterfly vertebrae.

4. Eye Findings: Posterior embryotoxon.

5. Facial Features: The characteristic "triangular" facial appearance.

If a genetic mutation in JAG1 or NOTCH2 is found, the diagnosis is confirmed even if the patient only has one or two of these features. This "genetics-first" approach allows for earlier intervention, especially for children who may only show heart or kidney issues initially.